Diff of the two buildlogs: -- --- b1/build.log 2024-01-20 01:17:59.644104599 +0000 +++ b2/build.log 2024-01-20 02:10:08.575608253 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Feb 20 19:23:38 -12 2025 -I: pbuilder-time-stamp: 1740122618 +I: Current time: Sat Jan 20 15:18:15 +14 2024 +I: pbuilder-time-stamp: 1705713495 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -34,51 +34,83 @@ dpkg-source: info: applying extra_float_digits I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/22977/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/8554/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jan 20 01:18 /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/8554/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/8554/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='67adab03f18f4f43a36bbb3713b8cf72' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='22977' - PS1='# ' - PS2='> ' + INVOCATION_ID=43aa6eac18194cc3bae1f71cfc5385c7 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=8554 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.BQZj5MCH/pbuilderrc_GTr4 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.BQZj5MCH/b1 --logfile b1/build.log rdkit_202209.3-1.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + 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.BQZj5MCH/pbuilderrc_5ayq --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.BQZj5MCH/b2 --logfile b2/build.log rdkit_202209.3-1.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos16-i386 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-686-pae #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) i686 GNU/Linux I: ls -l /bin total 6036 -rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash @@ -136,15 +168,15 @@ -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 22308 Jul 28 2023 run-parts + -rwxr-xr-x 1 root root 22308 Jul 28 23:46 run-parts -rwxr-xr-x 1 root root 133224 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash + lrwxrwxrwx 1 root root 9 Jan 20 01:18 sh -> /bin/bash -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty -rwsr-xr-x 1 root root 83492 Mar 23 2023 su -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync -rwxr-xr-x 1 root root 598456 Apr 6 2023 tar - -rwxr-xr-x 1 root root 13860 Jul 28 2023 tempfile + -rwxr-xr-x 1 root root 13860 Jul 28 23:46 tempfile -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch -rwxr-xr-x 1 root root 34664 Sep 20 2022 true -rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server @@ -164,7 +196,7 @@ -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew -I: user script /srv/workspace/pbuilder/22977/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/8554/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -605,7 +637,7 @@ Get: 330 http://deb.debian.org/debian bookworm/main i386 texlive-latex-recommended all 2022.20230122-3 [8880 kB] Get: 331 http://deb.debian.org/debian bookworm/main i386 texlive-pictures all 2022.20230122-3 [15.8 MB] Get: 332 http://deb.debian.org/debian bookworm/main i386 texlive-latex-extra all 2022.20230122-4 [19.2 MB] -Fetched 393 MB in 4s (97.2 MB/s) +Fetched 393 MB in 26s (15.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package m4. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18156 files and directories currently installed.) @@ -1664,8 +1696,8 @@ Setting up tzdata (2023c-5+deb12u1) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Feb 21 07:24:34 UTC 2025. -Universal Time is now: Fri Feb 21 07:24:34 UTC 2025. +Local time is now: Sat Jan 20 01:22:32 UTC 2024. +Universal Time is now: Sat Jan 20 01:22:32 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up xtrans-dev (1.4.0-1) ... @@ -2019,7 +2051,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/rdkit-202209.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../rdkit_202209.3-1_source.changes +I: user script /srv/workspace/pbuilder/8554/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/8554/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/rdkit-202209.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../rdkit_202209.3-1_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202209.3-1 dpkg-buildpackage: info: source distribution unstable @@ -2161,130 +2197,130 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/rdkit-202209.3' dh_auto_build - cd obj-i686-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-i686-linux-gnu && make -j7 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202209.3 -B/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/CMakeFiles /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f External/catch/CMakeFiles/catch.dir/build.make External/catch/CMakeFiles/catch.dir/depend -make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/depend -make -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/depend -make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/depend cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/External/catch /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/catch /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/catch/CMakeFiles/catch.dir/DependInfo.cmake --color= -make -f External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build.make External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/depend +make -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/External/INCHI-API /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/INCHI-API /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/INCHI-API/CMakeFiles/inchi_support.dir/DependInfo.cmake --color= -make -f External/GA/CMakeFiles/ga.dir/build.make External/GA/CMakeFiles/ga.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/External/CoordGen /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/CoordGen/CMakeFiles/coordgen_support.dir/DependInfo.cmake --color= -make -f Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build.make Code/RDGeneral/CMakeFiles/rdkitCatch.dir/depend +make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f External/catch/CMakeFiles/catch.dir/build.make External/catch/CMakeFiles/catch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/depend cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/External/RingFamilies /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/RingFamilies /build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/External/GA /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/GA /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/GA/CMakeFiles/ga.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/rdkitCatch.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDStreams /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDStreams /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDStreams/CMakeFiles/RDStreams.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/DependInfo.cmake --color= +make -f External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build.make External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/depend +make[4]: Nothing to be done for 'External/catch/CMakeFiles/catch.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/External/RingFamilies /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/RingFamilies /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/DependInfo.cmake --color= +make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/INCHI-API && /usr/bin/cmake -E copy /build/reproducible-path/rdkit-202209.3/External/INCHI-API/python/noinchi.py /build/reproducible-path/rdkit-202209.3/rdkit/Chem/inchi.py 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-202209.3/obj-i686-linux-gnu' -make -f External/catch/CMakeFiles/catch.dir/build.make External/catch/CMakeFiles/catch.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make[4]: Nothing to be done for 'External/CoordGen/CMakeFiles/coordgen_support.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f External/GA/CMakeFiles/ga.dir/build.make External/GA/CMakeFiles/ga.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Nothing to be done for 'External/catch/CMakeFiles/catch.dir/build'. +make -f External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build.make External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build.make Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/INCHI-API && /usr/bin/cmake -E copy /build/reproducible-path/rdkit-202209.3/External/INCHI-API/python/noinchi.py /build/reproducible-path/rdkit-202209.3/rdkit/Chem/inchi.py -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make[4]: Nothing to be done for 'External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 0%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o +[ 0%] Built target catch +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o -MF CMakeFiles/RDGeneral.dir/Invariant.cpp.o.d -o CMakeFiles/RDGeneral.dir/Invariant.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.cpp +[ 0%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o -MF CMakeFiles/RDGeneral.dir/types.cpp.o.d -o CMakeFiles/RDGeneral.dir/types.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/types.cpp +[ 0%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o +[ 0%] Built target inchi_support +make -f External/GA/CMakeFiles/ga.dir/build.make External/GA/CMakeFiles/ga.dir/depend +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o -MF CMakeFiles/RDGeneral.dir/utils.cpp.o.d -o CMakeFiles/RDGeneral.dir/utils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/utils.cpp +[ 0%] Built target coordgen_support make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build.make Code/RDGeneral/CMakeFiles/rdkitCatch.dir/depend +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/External/GA /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/GA /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/GA/CMakeFiles/ga.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Nothing to be done for 'External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build'. -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/build -make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/rdkitCatch.dir/DependInfo.cmake --color= +[ 0%] Built target ringdecomposerlib_support +make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDStreams /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDStreams /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDStreams/CMakeFiles/RDStreams.dir/DependInfo.cmake --color= +[ 0%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o -MF CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o.d -o CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDGeneralExceptions.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f External/GA/CMakeFiles/ga.dir/build.make External/GA/CMakeFiles/ga.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build.make Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 0%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o [ 0%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/StringChromosome.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT External/GA/CMakeFiles/ga.dir/ga/StringChromosome.cpp.o -MF CMakeFiles/ga.dir/ga/StringChromosome.cpp.o.d -o CMakeFiles/ga.dir/ga/StringChromosome.cpp.o -c /build/reproducible-path/rdkit-202209.3/External/GA/ga/StringChromosome.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o -MF CMakeFiles/RDGeneral.dir/types.cpp.o.d -o CMakeFiles/RDGeneral.dir/types.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/types.cpp -[ 0%] Built target coordgen_support -[ 0%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/rdkitCatch.dir/catch_main.cpp.o -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 1%] Built target ringdecomposerlib_support -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o -MF CMakeFiles/RDGeneral.dir/Invariant.cpp.o.d -o CMakeFiles/RDGeneral.dir/Invariant.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.cpp -[ 1%] Built target catch -[ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/Chromosome.cpp.o -[ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/rdkitCatch.dir/catch_main.cpp.o -MF CMakeFiles/rdkitCatch.dir/catch_main.cpp.o.d -o CMakeFiles/rdkitCatch.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/catch_main.cpp -[ 2%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o -[ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o -[ 3%] Building CXX object Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o +[ 2%] Building CXX object Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDStreams && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RDSTREAMS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDStreams_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o -MF CMakeFiles/RDStreams.dir/streams.cpp.o.d -o CMakeFiles/RDStreams.dir/streams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDStreams/streams.cpp +[ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o -MF CMakeFiles/RDGeneral.dir/RDLog.cpp.o.d -o CMakeFiles/RDGeneral.dir/RDLog.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.cpp +[ 2%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/Chromosome.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT External/GA/CMakeFiles/ga.dir/ga/Chromosome.cpp.o -MF CMakeFiles/ga.dir/ga/Chromosome.cpp.o.d -o CMakeFiles/ga.dir/ga/Chromosome.cpp.o -c /build/reproducible-path/rdkit-202209.3/External/GA/ga/Chromosome.cpp -[ 3%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o -[ 3%] Building CXX object External/GA/CMakeFiles/ga.dir/util/RandomUtil.cpp.o +[ 2%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/External/GA/ga/IntegerStringChromosomePolicy.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o -MF CMakeFiles/RDGeneral.dir/utils.cpp.o.d -o CMakeFiles/RDGeneral.dir/utils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/utils.cpp -[ 3%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDStreams && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RDSTREAMS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDStreams_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o -MF CMakeFiles/RDStreams.dir/streams.cpp.o.d -o CMakeFiles/RDStreams.dir/streams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDStreams/streams.cpp +[ 3%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/RDGeneral/LocaleSwitcher.cpp +[ 4%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT External/GA/CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o -MF CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o.d -o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o -c /build/reproducible-path/rdkit-202209.3/External/GA/ga/BinaryStringChromosomePolicy.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o -MF CMakeFiles/hc.dir/hc.c.o.d -o CMakeFiles/hc.dir/hc.c.o -c /build/reproducible-path/rdkit-202209.3/Code/ML/Cluster/Murtagh/hc.c +[ 4%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/RDGeneral/versions.cpp +[ 4%] Building CXX object External/GA/CMakeFiles/ga.dir/util/RandomUtil.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT External/GA/CMakeFiles/ga.dir/util/RandomUtil.cpp.o -MF CMakeFiles/ga.dir/util/RandomUtil.cpp.o.d -o CMakeFiles/ga.dir/util/RandomUtil.cpp.o -c /build/reproducible-path/rdkit-202209.3/External/GA/util/RandomUtil.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o -MF CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o.d -o CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDGeneralExceptions.cpp -[ 3%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o -[ 3%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o -[ 3%] Built target inchi_support -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o -MF CMakeFiles/RDGeneral.dir/RDLog.cpp.o.d -o CMakeFiles/RDGeneral.dir/RDLog.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.cpp -[ 4%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o -MF CMakeFiles/hc.dir/hcdriver.c.o.d -o CMakeFiles/hc.dir/hcdriver.c.o -c /build/reproducible-path/rdkit-202209.3/Code/ML/Cluster/Murtagh/hcdriver.c -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/RDGeneral/LocaleSwitcher.cpp [ 4%] Building CXX object External/GA/CMakeFiles/ga.dir/util/Util.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/External/GA/util/Util.cpp -[ 4%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/RDGeneral/versions.cpp +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-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 4%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o -MF CMakeFiles/hc.dir/hc.c.o.d -o CMakeFiles/hc.dir/hc.c.o -c /build/reproducible-path/rdkit-202209.3/Code/ML/Cluster/Murtagh/hc.c +[ 4%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o -MF CMakeFiles/hc.dir/hcdriver.c.o.d -o CMakeFiles/hc.dir/hcdriver.c.o -c /build/reproducible-path/rdkit-202209.3/Code/ML/Cluster/Murtagh/hcdriver.c [ 5%] Linking C shared library ../../../../lib/libRDKithc.so cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/hc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKithc.so.1 -o ../../../../lib/libRDKithc.so.1.2022.09.3 CMakeFiles/hc.dir/hc.c.o CMakeFiles/hc.dir/hcdriver.c.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libRDKithc.so.1.2022.09.3 ../../../../lib/libRDKithc.so.1 ../../../../lib/libRDKithc.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 5%] Built target hc -[ 5%] Linking CXX shared library ../../lib/libRDKitga.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/GA && /usr/bin/cmake -E cmake_link_script CMakeFiles/ga.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitga.so.1 -o ../../lib/libRDKitga.so.1.2022.09.3 CMakeFiles/ga.dir/ga/StringChromosome.cpp.o CMakeFiles/ga.dir/ga/Chromosome.cpp.o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/util/RandomUtil.cpp.o CMakeFiles/ga.dir/util/Util.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/GA && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitga.so.1.2022.09.3 ../../lib/libRDKitga.so.1 ../../lib/libRDKitga.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 5%] Built target ga [ 5%] Linking CXX shared library ../../lib/libRDKitRDStreams.so cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDStreams.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDStreams.so.1 -o ../../lib/libRDKitRDStreams.so.1.2022.09.3 CMakeFiles/RDStreams.dir/streams.cpp.o /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDStreams.so.1.2022.09.3 ../../lib/libRDKitRDStreams.so.1 ../../lib/libRDKitRDStreams.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 5%] Built target RDStreams +[ 5%] Linking CXX shared library ../../lib/libRDKitga.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/GA && /usr/bin/cmake -E cmake_link_script CMakeFiles/ga.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitga.so.1 -o ../../lib/libRDKitga.so.1.2022.09.3 CMakeFiles/ga.dir/ga/StringChromosome.cpp.o CMakeFiles/ga.dir/ga/Chromosome.cpp.o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/util/RandomUtil.cpp.o CMakeFiles/ga.dir/util/Util.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/GA && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitga.so.1.2022.09.3 ../../lib/libRDKitga.so.1 ../../lib/libRDKitga.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 5%] Built target ga [ 5%] Linking CXX shared library ../../lib/libRDKitRDGeneral.so cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeneral.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeneral.so.1 -o ../../lib/libRDKitRDGeneral.so.1.2022.09.3 CMakeFiles/RDGeneral.dir/Invariant.cpp.o CMakeFiles/RDGeneral.dir/types.cpp.o CMakeFiles/RDGeneral.dir/utils.cpp.o CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o CMakeFiles/RDGeneral.dir/RDLog.cpp.o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o CMakeFiles/RDGeneral.dir/versions.cpp.o -ldl @@ -2292,155 +2328,63 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 5%] Built target RDGeneral make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend -make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend -make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend -make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake --color= +make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake --color= -make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend +make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDBoost /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDBoost /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake --color= -make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake --color= -make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.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-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics /build/reproducible-path/rdkit-202209.3/obj-i686-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[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Catalogs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Catalogs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake --color= -make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Query /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Query /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Query/CMakeFiles/testQuery.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataManip/MetricMatrixCalc /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/build -make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake --color= 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-202209.3/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/build -make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/build +[ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o -MF CMakeFiles/DataStructs.dir/BitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/BitVect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/BitVect.cpp +[ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/SparseBitVect.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build +make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/build +[ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o +[ 5%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/ExplicitBitVect.cpp +[ 5%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDBoost && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDBoost_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDBOOST_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o -MF CMakeFiles/RDBoost.dir/Wrap.cpp.o.d -o CMakeFiles/RDBoost.dir/Wrap.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DEigenSolvers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_EIGENSOLVERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -MF CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o.d -o CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/EigenSolvers/PowerEigenSolver.cpp +[ 5%] Building CXX object Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/testDict.dir/testDict.cpp.o -MF CMakeFiles/testDict.dir/testDict.cpp.o.d -o CMakeFiles/testDict.dir/testDict.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testDict.cpp +[ 5%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_link_script CMakeFiles/EigenSolvers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitEigenSolvers.so.1 -o ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' +[ 5%] Built target EigenSolvers +make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 5%] Building CXX object Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o -[ 5%] Building CXX object Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -[ 5%] Building CXX object Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -MF CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o.d -o CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testConcurrentQueue.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/Numerics/testMatrices.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/testDict.dir/testDict.cpp.o -MF CMakeFiles/testDict.dir/testDict.cpp.o.d -o CMakeFiles/testDict.dir/testDict.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testDict.cpp -[ 5%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o [ 5%] Building CXX object Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o -[ 5%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DEigenSolvers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_EIGENSOLVERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -MF CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o.d -o CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/EigenSolvers/PowerEigenSolver.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDBoost && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDBoost_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDBOOST_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o -MF CMakeFiles/RDBoost.dir/Wrap.cpp.o.d -o CMakeFiles/RDBoost.dir/Wrap.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.cpp cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o -MF CMakeFiles/testRDValue.dir/testRDValue.cpp.o.d -o CMakeFiles/testRDValue.dir/testRDValue.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testRDValue.cpp -[ 5%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o -[ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o -[ 5%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -[ 5%] Building CXX object Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -[ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -[ 5%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -[ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -[ 5%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o -MF CMakeFiles/Catalogs.dir/Catalog.cpp.o.d -o CMakeFiles/Catalogs.dir/Catalog.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Catalogs/Catalog.cpp -[ 5%] Building CXX object Code/Query/CMakeFiles/testQuery.dir/test.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -MF CMakeFiles/Catalogs.dir/CatalogParams.cpp.o.d -o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Catalogs/CatalogParams.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o -MF CMakeFiles/DataStructs.dir/BitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/BitVect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/BitVect.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/DistPicker.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/SparseBitVect.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -MF CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o.d -o CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataManip/MetricMatrixCalc/testMatCalc.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/Catalogs/CatalogEntry.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/ExplicitBitVect.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Query && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Query/CMakeFiles/testQuery.dir/test.cpp.o -MF CMakeFiles/testQuery.dir/test.cpp.o.d -o CMakeFiles/testQuery.dir/test.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Query/test.cpp -[ 5%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/MaxMinPicker.cpp -[ 5%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/SimDivPickers/HierarchicalClusterPicker.cpp -[ 5%] Linking CXX executable testMatCalc -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatCalc.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -o testMatCalc ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 5%] Built target testMatCalc [ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o -MF CMakeFiles/DataStructs.dir/Utils.cpp.o.d -o CMakeFiles/DataStructs.dir/Utils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Utils.cpp [ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o -[ 6%] Linking CXX executable testConcurrentQueue -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConcurrentQueue.dir/link.txt --verbose=1 cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o -MF CMakeFiles/DataStructs.dir/base64.cpp.o.d -o CMakeFiles/DataStructs.dir/base64.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/base64.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -o testConcurrentQueue ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 6%] Built target testConcurrentQueue [ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o -MF CMakeFiles/DataStructs.dir/BitOps.cpp.o.d -o CMakeFiles/DataStructs.dir/BitOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/BitOps.cpp [ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -MF CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o.d -o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/DiscreteDistMat.cpp -[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -MF CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o.d -o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/DiscreteValueVect.cpp -[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/DataStructs/FPBReader.cpp -[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/MultiFPBReader.cpp -[ 6%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_link_script CMakeFiles/EigenSolvers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitEigenSolvers.so.1 -o ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 6%] Built target EigenSolvers -[ 7%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/SimDivPickers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSimDivPickers.so.1 -o ../../lib/libRDKitSimDivPickers.so.1.2022.09.3 CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o ../../lib/libRDKithc.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.so.1.2022.09.3 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 7%] Built target SimDivPickers -make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 7%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/SimDivPickers/testPickers.cpp -[ 7%] Linking CXX shared library ../../lib/libRDKitCatalogs.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2022.09.3 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 7%] Built target Catalogs In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2458,126 +2402,81 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 8%] Linking CXX executable testMatrices -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 8%] Built target testMatrices -[ 8%] Linking CXX executable testQuery -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Query && /usr/bin/cmake -E cmake_link_script CMakeFiles/testQuery.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testQuery.dir/test.cpp.o -o testQuery ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 8%] Built target testQuery -[ 8%] Linking CXX shared library ../../lib/libRDKitRDBoost.so +[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -MF CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o.d -o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/DiscreteValueVect.cpp +[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/DataStructs/FPBReader.cpp +[ 6%] Linking CXX shared library ../../lib/libRDKitRDBoost.so cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDBoost && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDBoost.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDBoost.so.1 -o ../../lib/libRDKitRDBoost.so.1.2022.09.3 CMakeFiles/RDBoost.dir/Wrap.cpp.o ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDBoost && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../lib/libRDKitRDBoost.so.1 ../../lib/libRDKitRDBoost.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 8%] Built target RDBoost -make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend -make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDBoost/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/DependInfo.cmake --color= +[ 6%] Built target RDBoost +make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build +make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 6%] Building CXX object Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -MF CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o.d -o CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testConcurrentQueue.cpp +[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/MultiFPBReader.cpp +make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDBoost/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 8%] Building CXX object Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DClustering_EXPORTS -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o -MF CMakeFiles/Clustering.dir/Clustering.cpp.o.d -o CMakeFiles/Clustering.dir/Clustering.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ML/Cluster/Murtagh/Clustering.cpp -[ 8%] Building CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o +[ 6%] Building CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDBoost/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdBase_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o -MF CMakeFiles/rdBase.dir/RDBase.cpp.o.d -o CMakeFiles/rdBase.dir/RDBase.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap/RDBase.cpp -[ 8%] Linking CXX executable testSimDivPickers -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSimDivPickers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -o testSimDivPickers ../../lib/libRDKitSimDivPickers.so.1.2022.09.3 ../../lib/libRDKithc.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 8%] Built target testSimDivPickers -[ 8%] Linking CXX shared library ../../lib/libRDKitDataStructs.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDataStructs.so.1 -o ../../lib/libRDKitDataStructs.so.1.2022.09.3 CMakeFiles/DataStructs.dir/BitVect.cpp.o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o CMakeFiles/DataStructs.dir/Utils.cpp.o CMakeFiles/DataStructs.dir/base64.cpp.o CMakeFiles/DataStructs.dir/BitOps.cpp.o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/DataStructs.dir/FPBReader.cpp.o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so +[ 6%] Linking CXX executable testConcurrentQueue +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConcurrentQueue.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -o testConcurrentQueue ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 8%] Built target DataStructs -make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend -make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend -make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend -make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Geometry /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake --color= -make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake --color= -make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake --color= -make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.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-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/DependInfo.cmake --color= +[ 6%] Built target testConcurrentQueue +make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/InfoTheory /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build -make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/CMakeFiles/testMatrices.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build +make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 6%] Building CXX object Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/Numerics/testMatrices.cpp +make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Catalogs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Catalogs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build +make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 6%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o -MF CMakeFiles/Catalogs.dir/Catalog.cpp.o.d -o CMakeFiles/Catalogs.dir/Catalog.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Catalogs/Catalog.cpp +[ 6%] Linking CXX executable testDict +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDict.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDict.dir/testDict.cpp.o -o testDict ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build +[ 6%] Built target testDict +make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Query /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Query /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Query/CMakeFiles/testQuery.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build +make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 6%] Building CXX object Code/Query/CMakeFiles/testQuery.dir/test.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Query && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Query/CMakeFiles/testQuery.dir/test.cpp.o -MF CMakeFiles/testQuery.dir/test.cpp.o.d -o CMakeFiles/testQuery.dir/test.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Query/test.cpp +[ 7%] Linking CXX executable testMatrices +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 7%] Built target testMatrices +make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -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-202209.3/obj-i686-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 9%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -[ 9%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -[ 9%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o -[ 9%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -[ 10%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -[ 10%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -[ 10%] Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/MaxMinPicker.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -MF CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/DiscreteValueVect.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/Geometry/point.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -MF CMakeFiles/cDataStructs.dir/DataStructs.cpp.o.d -o CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/DataStructs.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/DataStructs/testDatastructs.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/LeaderPicker.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -MF CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/SparseIntVect.cpp -[ 10%] Building CXX object Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o -[ 10%] Building CXX object Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/DataStructs/testFPB.cpp -[ 10%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/testMultiFPB.dir/testMultiFPB.cpp.o -MF CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o.d -o CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/testMultiFPB.cpp -[ 10%] Building CXX object Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/InfoTheory && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DInfoTheory_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_INFOTHEORY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/ML/InfoTheory/InfoBitRanker.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMetricMatrixCalc_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -MF CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o.d -o CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp -[ 10%] Linking CXX executable testDict -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDict.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDict.dir/testDict.cpp.o -o testDict ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataManip/MetricMatrixCalc /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 10%] Built target testDict -[ 10%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_SparseBV.cpp +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-202209.3/obj-i686-linux-gnu' +[ 7%] Building CXX object Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -MF CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o.d -o CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataManip/MetricMatrixCalc/testMatCalc.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2596,13 +2495,81 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 10%] Linking CXX executable testRDValue +[ 7%] Linking CXX shared library ../../lib/libRDKitDataStructs.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDataStructs.so.1 -o ../../lib/libRDKitDataStructs.so.1.2022.09.3 CMakeFiles/DataStructs.dir/BitVect.cpp.o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o CMakeFiles/DataStructs.dir/Utils.cpp.o CMakeFiles/DataStructs.dir/base64.cpp.o CMakeFiles/DataStructs.dir/BitOps.cpp.o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/DataStructs.dir/FPBReader.cpp.o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 7%] Built target DataStructs +make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' +[ 7%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/DistPicker.cpp +[ 7%] Linking CXX executable testRDValue cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDValue.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRDValue.dir/testRDValue.cpp.o -o testRDValue ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 7%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -MF CMakeFiles/Catalogs.dir/CatalogParams.cpp.o.d -o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Catalogs/CatalogParams.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 10%] Built target testRDValue -[ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/Geometry/Transform2D.cpp +[ 7%] Built target testRDValue +make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 7%] Building CXX object Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DClustering_EXPORTS -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o -MF CMakeFiles/Clustering.dir/Clustering.cpp.o.d -o CMakeFiles/Clustering.dir/Clustering.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ML/Cluster/Murtagh/Clustering.cpp +[ 7%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/Catalogs/CatalogEntry.cpp +[ 7%] Linking CXX executable testMatCalc +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatCalc.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -o testMatCalc ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 7%] Linking CXX shared library ../../lib/libRDKitCatalogs.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2022.09.3 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 7%] Built target testMatCalc +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-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/InfoTheory /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +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-202209.3/obj-i686-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 7%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/InfoTheory && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DInfoTheory_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_INFOTHEORY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/ML/InfoTheory/InfoBitRanker.cpp +[ 7%] Built target Catalogs +[ 7%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/MaxMinPicker.cpp +[ 7%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/SimDivPickers/HierarchicalClusterPicker.cpp +[ 7%] Linking CXX executable testQuery +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Query && /usr/bin/cmake -E cmake_link_script CMakeFiles/testQuery.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testQuery.dir/test.cpp.o -o testQuery ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 7%] Built target testQuery +make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Geometry /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 7%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/Geometry/point.cpp +make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 7%] Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/DataStructs/testDatastructs.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2620,69 +2587,51 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/DiscreteValueVect.cpp:11: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/Transform3D.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 10%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so +[ 8%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/SimDivPickers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSimDivPickers.so.1 -o ../../lib/libRDKitSimDivPickers.so.1.2022.09.3 CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o ../../lib/libRDKithc.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.so.1.2022.09.3 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so +[ 8%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/Geometry/Transform2D.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 8%] Built target SimDivPickers +make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 8%] Building CXX object Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/DataStructs/testFPB.cpp +[ 8%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/Clustering.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/Cluster/Clustering.so CMakeFiles/Clustering.dir/Clustering.cpp.o ../../../../lib/libRDKithc.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so +[ 8%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_link_script CMakeFiles/InfoTheory.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitInfoTheory.so.1 -o ../../../lib/libRDKitInfoTheory.so.1.2022.09.3 CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 10%] Built target Clustering -[ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/Geometry/UniformGrid3D.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/LeaderPicker.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ +[ 8%] Built target Clustering +make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitInfoTheory.so.1.2022.09.3 ../../../lib/libRDKitInfoTheory.so.1 ../../../lib/libRDKitInfoTheory.so +[ 8%] Building CXX object Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/testMultiFPB.dir/testMultiFPB.cpp.o -MF CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o.d -o CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/testMultiFPB.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 8%] Built target InfoTheory +make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 9%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -MF CMakeFiles/cDataStructs.dir/DataStructs.cpp.o.d -o CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/DataStructs.cpp +[ 9%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/Transform3D.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2701,6 +2650,36 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 9%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/Geometry/UniformGrid3D.cpp +[ 9%] Linking CXX executable testFPB +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFPB.dir/testFPB.cpp.o -o testFPB ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 9%] Built target testFPB +make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake --color= +[ 9%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -MF CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/DiscreteValueVect.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 9%] Building CXX object Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMetricMatrixCalc_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -MF CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o.d -o CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp +[ 9%] Linking CXX executable testMultiFPB +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultiFPB.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -o testMultiFPB ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 9%] Built target testMultiFPB +make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 9%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/SimDivPickers/testPickers.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2715,7 +2694,7 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/MaxMinPicker.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -2733,39 +2712,30 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/SparseIntVect.cpp:11: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 10%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_link_script CMakeFiles/InfoTheory.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitInfoTheory.so.1 -o ../../../lib/libRDKitInfoTheory.so.1.2022.09.3 CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitInfoTheory.so.1.2022.09.3 ../../../lib/libRDKitInfoTheory.so.1 ../../../lib/libRDKitInfoTheory.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 10%] Built target InfoTheory -[ 10%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_SparseBV.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/DiscreteValueVect.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 10%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp -[ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o +[ 9%] Linking CXX executable testDataStructs +[ 9%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/Geometry/GridUtils.cpp +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 9%] Built target testDataStructs +make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 10%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/MaxMinPicker.cpp +[ 10%] Linking CXX executable testSimDivPickers +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSimDivPickers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -o testSimDivPickers ../../lib/libRDKitSimDivPickers.so.1.2022.09.3 ../../lib/libRDKithc.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 10%] Built target testSimDivPickers make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake --color= @@ -2787,8 +2757,16 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 12%] Building CXX object Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/Data && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcQuantize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o -MF CMakeFiles/cQuantize.dir/cQuantize.cpp.o.d -o CMakeFiles/cQuantize.dir/cQuantize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ML/Data/cQuantize.cpp -[ 12%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_BitOps.cpp +[ 12%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeometryLib.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 CMakeFiles/RDGeometryLib.dir/point.cpp.o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 12%] Built target RDGeometryLib +[ 12%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -MF CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/SparseIntVect.cpp +[ 12%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -MF CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2803,30 +2781,28 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp:13: + from /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp:12: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/MaxMinPicker.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 12%] Linking CXX executable testMultiFPB -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultiFPB.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -o testMultiFPB ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 12%] Built target testMultiFPB -[ 12%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_FPB.cpp -[ 12%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_Utils.cpp -[ 12%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -MF CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp -[ 12%] Linking CXX executable testFPB -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFPB.dir/testFPB.cpp.o -o testFPB ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 12%] Built target testFPB -[ 12%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -MF CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp -[ 12%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2837,37 +2813,13 @@ from /usr/include/boost/smart_ptr.hpp:19, from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp:10: + from /build/reproducible-path/rdkit-202209.3/Code/ML/Data/cQuantize.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 12%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeometryLib.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 CMakeFiles/RDGeometryLib.dir/point.cpp.o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 12%] Built target RDGeometryLib -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[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/build -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-202209.3/obj-i686-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o -[ 12%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment && /usr/bin/c++ -DAlignment_EXPORTS -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o -MF CMakeFiles/Alignment.dir/AlignPoints.cpp.o.d -o CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/AlignPoints.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Atom.cpp -[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/QueryAtom.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2882,7 +2834,7 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/SparseIntVect.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -2900,10 +2852,23 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_BitOps.cpp:10: + from /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 12%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/LeaderPicker.cpp +[ 12%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/Data && /usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o ../../../lib/libRDKitInfoTheory.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 12%] Built target cQuantize +[ 12%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp +[ 12%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp +[ 12%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -MF CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2911,16 +2876,17 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/ML/Data/cQuantize.cpp:11: + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp:13: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2935,12 +2901,10 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/LeaderPicker.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o -MF CMakeFiles/GraphMol.dir/QueryBond.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryBond.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/QueryBond.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2951,13 +2915,10 @@ from /usr/include/boost/smart_ptr.hpp:19, from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_Utils.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2968,18 +2929,44 @@ from /usr/include/boost/smart_ptr.hpp:19, from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_FPB.cpp:10: + from /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 12%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/Data && /usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o ../../../lib/libRDKitInfoTheory.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake --color= +[ 12%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_SparseBV.cpp +[ 12%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 12%] Built target cQuantize +make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Atom.cpp +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -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.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 12%] Built target rdInfoTheory +make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' +[ 12%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment && /usr/bin/c++ -DAlignment_EXPORTS -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o -MF CMakeFiles/Alignment.dir/AlignPoints.cpp.o.d -o CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/AlignPoints.cpp +[ 12%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/SimDivFilters/rdSimDivPickers.so CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o ../../../lib/libRDKitSimDivPickers.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKithc.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 12%] Built target rdSimDivPickers make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Geometry /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake --color= @@ -2988,6 +2975,9 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 12%] Building CXX object Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o -MF CMakeFiles/testTransforms.dir/testTransforms.cpp.o.d -o CMakeFiles/testTransforms.dir/testTransforms.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/testTransforms.cpp +[ 12%] Linking CXX shared library ../../../lib/libRDKitAlignment.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2022.09.3 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2998,33 +2988,13 @@ from /usr/include/boost/smart_ptr.hpp:19, from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_SparseBV.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 12%] Linking CXX shared library ../../../lib/libRDKitAlignment.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2022.09.3 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 12%] Built target Alignment @@ -3036,59 +3006,86 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 13%] Building CXX object Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o -MF CMakeFiles/testGrid.dir/testGrid.cpp.o.d -o CMakeFiles/testGrid.dir/testGrid.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/testGrid.cpp +[ 14%] Linking CXX executable testTransforms +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testTransforms.dir/testTransforms.cpp.o -o testTransforms ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 14%] Built target testTransforms make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' -[ 13%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o +[ 14%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o -MF CMakeFiles/rdGeometry.dir/Point.cpp.o.d -o CMakeFiles/rdGeometry.dir/Point.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/Point.cpp -[ 13%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/SimDivFilters/rdSimDivPickers.so CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o ../../../lib/libRDKitSimDivPickers.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKithc.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 14%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp +[ 14%] Linking CXX executable testGrid +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGrid.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGrid.dir/testGrid.cpp.o -o testGrid ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 13%] Built target rdSimDivPickers +[ 14%] Built target testGrid make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 13%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -[ 13%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o +[ 14%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o -MF CMakeFiles/testAlignment.dir/testAlignment.cpp.o.d -o CMakeFiles/testAlignment.dir/testAlignment.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/testAlignment.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -MF CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/UniformGrid3D.cpp -[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o -MF CMakeFiles/GraphMol.dir/Bond.cpp.o.d -o CMakeFiles/GraphMol.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Bond.cpp -[ 13%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -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.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/QueryAtom.cpp +[ 14%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_BitOps.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/Point.cpp:11: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 15%] Linking CXX executable testAlignment +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAlignment.dir/link.txt --verbose=1 +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp:10: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAlignment.dir/testAlignment.cpp.o -o testAlignment ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 13%] Built target rdInfoTheory +[ 15%] Built target testAlignment make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 13%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o +[ 15%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdAlignment_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -MF CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o.d -o CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/rdAlignment.cpp -[ 13%] Linking CXX executable testDataStructs -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 13%] Built target testDataStructs -make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 13%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemicalFeatures_EXPORTS -DRDKIT_CHEMICALFEATURES_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/ChemicalFeatures/FreeChemicalFeature.cpp -[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o -MF CMakeFiles/GraphMol.dir/MolOps.cpp.o.d -o CMakeFiles/GraphMol.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolOps.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3103,13 +3100,12 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/UniformGrid3D.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_BitOps.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 13%] Linking CXX executable testGrid -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGrid.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGrid.dir/testGrid.cpp.o -o testGrid ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o -MF CMakeFiles/GraphMol.dir/QueryBond.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryBond.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/QueryBond.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3124,48 +3120,46 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/Point.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 15%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_FPB.cpp +[ 15%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -MF CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/UniformGrid3D.cpp +[ 15%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAlignment.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Numerics/rdAlignment.so CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o ../../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 13%] Built target testGrid -[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o -MF CMakeFiles/GraphMol.dir/FindRings.cpp.o.d -o CMakeFiles/GraphMol.dir/FindRings.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FindRings.cpp -[ 13%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -MF CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o.d -o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/rdGeometry.cpp -[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o -MF CMakeFiles/GraphMol.dir/ROMol.cpp.o.d -o CMakeFiles/GraphMol.dir/ROMol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ROMol.cpp -[ 14%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemicalFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemicalFeatures.so.1 -o ../../lib/libRDKitChemicalFeatures.so.1.2022.09.3 CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitChemicalFeatures.so.1.2022.09.3 ../../lib/libRDKitChemicalFeatures.so.1 ../../lib/libRDKitChemicalFeatures.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 14%] Built target ChemicalFeatures -make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend +[ 15%] Built target rdAlignment +make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/DependInfo.cmake --color= -[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o -MF CMakeFiles/GraphMol.dir/RWMol.cpp.o.d -o CMakeFiles/GraphMol.dir/RWMol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RWMol.cpp +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build +make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 14%] Building CXX object Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -MF CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o.d -o CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/testChemicalFeatures.cpp -[ 15%] Linking CXX executable testTransforms -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testTransforms.dir/testTransforms.cpp.o -o testTransforms ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 15%] Built target testTransforms -[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -MF CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o.d -o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PeriodicTable.cpp -[ 16%] Linking CXX executable testAlignment -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAlignment.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAlignment.dir/testAlignment.cpp.o -o testAlignment ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 16%] Built target testAlignment -[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -MF CMakeFiles/GraphMol.dir/atomic_data.cpp.o.d -o CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/atomic_data.cpp +[ 15%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemicalFeatures_EXPORTS -DRDKIT_CHEMICALFEATURES_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/ChemicalFeatures/FreeChemicalFeature.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_FPB.cpp:10: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o -MF CMakeFiles/GraphMol.dir/Bond.cpp.o.d -o CMakeFiles/GraphMol.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Bond.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3180,48 +3174,35 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/UniformGrid3D.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o -MF CMakeFiles/GraphMol.dir/QueryOps.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/QueryOps.cpp -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FindRings.cpp: In function 'void RDKit::MolOps::findRingFamilies(const RDKit::ROMol&)': -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FindRings.cpp:1350:36: warning: unused parameter 'mol' [-Wunused-parameter] - 1350 | void findRingFamilies(const ROMol &mol) { - | ~~~~~~~~~~~~~^~~ -[ 16%] Linking CXX static library librdkitCatch.a -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkitCatch.dir/link.txt --verbose=1 -/usr/bin/ar qc librdkitCatch.a CMakeFiles/rdkitCatch.dir/catch_main.cpp.o -/usr/bin/ranlib librdkitCatch.a +[ 15%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemicalFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemicalFeatures.so.1 -o ../../lib/libRDKitChemicalFeatures.so.1.2022.09.3 CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitChemicalFeatures.so.1.2022.09.3 ../../lib/libRDKitChemicalFeatures.so.1 ../../lib/libRDKitChemicalFeatures.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 16%] Built target rdkitCatch -make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/depend +[ 15%] Built target ChemicalFeatures +make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build +make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 16%] Building CXX object Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/dictTestsCatch.dir/catch_dict.cpp.o -MF CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o.d -o CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/catch_dict.cpp -[ 16%] Linking CXX executable testChemicalFeatures +[ 15%] Building CXX object Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -MF CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o.d -o CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/testChemicalFeatures.cpp +[ 15%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_Utils.cpp +[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o -MF CMakeFiles/GraphMol.dir/MolOps.cpp.o.d -o CMakeFiles/GraphMol.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolOps.cpp +[ 15%] Linking CXX executable testChemicalFeatures cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -o testChemicalFeatures ../../lib/libRDKitChemicalFeatures.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 16%] Built target testChemicalFeatures -make -f Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/logTestsCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/logTestsCatch.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' -[ 16%] Building CXX object Code/RDGeneral/CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/RDGeneral/catch_logs.cpp -[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o -MF CMakeFiles/GraphMol.dir/MolPickler.cpp.o.d -o CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolPickler.cpp -[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o -MF CMakeFiles/GraphMol.dir/Canon.cpp.o.d -o CMakeFiles/GraphMol.dir/Canon.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Canon.cpp +[ 15%] Built target testChemicalFeatures +[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o -MF CMakeFiles/GraphMol.dir/FindRings.cpp.o.d -o CMakeFiles/GraphMol.dir/FindRings.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FindRings.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3232,80 +3213,64 @@ from /usr/include/boost/smart_ptr.hpp:19, from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/rdGeometry.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_Utils.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -MF CMakeFiles/GraphMol.dir/AtomIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/AtomIterators.cpp -[ 16%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAlignment.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Numerics/rdAlignment.so CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o ../../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 16%] Built target rdAlignment -make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Geometry /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' -[ 16%] Building CXX object Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/Geometry/catch_tests.cpp +[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o -MF CMakeFiles/GraphMol.dir/ROMol.cpp.o.d -o CMakeFiles/GraphMol.dir/ROMol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ROMol.cpp [ 17%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/cDataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DataStructs/cDataStructs.so CMakeFiles/cDataStructs.dir/DataStructs.cpp.o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 17%] Built target cDataStructs -make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 17%] Building CXX object Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o -MF CMakeFiles/testConrec.dir/testConrec.cpp.o.d -o CMakeFiles/testConrec.dir/testConrec.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/testConrec.cpp -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o -MF CMakeFiles/GraphMol.dir/BondIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/BondIterators.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/BondIterators.cpp -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Aromaticity.cpp -[ 18%] Linking CXX executable logTestsCatch -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/logTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -o logTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 18%] Built target logTestsCatch -make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 18%] Building CXX object Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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 CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/catch_tests.cpp -[ 18%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o -MF CMakeFiles/GraphMol.dir/RWMol.cpp.o.d -o CMakeFiles/GraphMol.dir/RWMol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RWMol.cpp +[ 17%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -MF CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o.d -o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/rdGeometry.cpp +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FindRings.cpp: In function 'void RDKit::MolOps::findRingFamilies(const RDKit::ROMol&)': +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FindRings.cpp:1350:36: warning: unused parameter 'mol' [-Wunused-parameter] + 1350 | void findRingFamilies(const ROMol &mol) { + | ~~~~~~~~~~~~~^~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/rdGeometry.cpp:11: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 17%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 18%] Built target rdGeometry -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o -MF CMakeFiles/GraphMol.dir/Kekulize.cpp.o.d -o CMakeFiles/GraphMol.dir/Kekulize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Kekulize.cpp -[ 18%] Linking CXX executable testConrec -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConrec.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testConrec.dir/testConrec.cpp.o -o testConrec ../RDGeneral/librdkitCatch.a ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 18%] Built target testConrec -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/ConjugHybrid.cpp -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/AddHs.cpp -[ 18%] Linking CXX executable geometryTestsCatch -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/geometryTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -o geometryTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 18%] Linking CXX executable dictTestsCatch -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/dictTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -o dictTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 17%] Built target rdGeometry +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -MF CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o.d -o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PeriodicTable.cpp +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -MF CMakeFiles/GraphMol.dir/atomic_data.cpp.o.d -o CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/atomic_data.cpp +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o -MF CMakeFiles/GraphMol.dir/QueryOps.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/QueryOps.cpp +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o -MF CMakeFiles/GraphMol.dir/MolPickler.cpp.o.d -o CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolPickler.cpp +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o -MF CMakeFiles/GraphMol.dir/Canon.cpp.o.d -o CMakeFiles/GraphMol.dir/Canon.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Canon.cpp +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -MF CMakeFiles/GraphMol.dir/AtomIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/AtomIterators.cpp +[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o -MF CMakeFiles/GraphMol.dir/BondIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/BondIterators.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/BondIterators.cpp /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolPickler.cpp: In instantiation of 'static RDKit::Atom* RDKit::MolPickler::_addAtomFromPickle(std::istream&, RDKit::ROMol*, RDGeom::Point3D&, int, bool) [with T = int; std::istream = std::basic_istream]': /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolPickler.cpp:1081:39: required from 'static void RDKit::MolPickler::_depickle(std::istream&, RDKit::ROMol*, int, int, unsigned int) [with T = int; std::istream = std::basic_istream]' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolPickler.cpp:854:27: required from here @@ -3316,12 +3281,20 @@ /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolPickler.cpp:1081:39: required from 'static void RDKit::MolPickler::_depickle(std::istream&, RDKit::ROMol*, int, int, unsigned int) [with T = unsigned char; std::istream = std::basic_istream]' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolPickler.cpp:856:33: required from here /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolPickler.cpp:1666:37: warning: comparison is always false due to limited range of data type [-Wtype-limits] -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 18%] Built target dictTestsCatch +[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Aromaticity.cpp +[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o -MF CMakeFiles/GraphMol.dir/Kekulize.cpp.o.d -o CMakeFiles/GraphMol.dir/Kekulize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Kekulize.cpp +[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/ConjugHybrid.cpp +[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/AddHs.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o -MF CMakeFiles/GraphMol.dir/Matrices.cpp.o.d -o CMakeFiles/GraphMol.dir/Matrices.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Matrices.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 18%] Built target geometryTestsCatch +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Kekulize.cpp: In function 'void RDKit::{anonymous}::markDbondCands(RDKit::RWMol&, const RDKit::INT_VECT&, boost::dynamic_bitset<>&, RDKit::INT_VECT&, RDKit::INT_VECT&)': +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Kekulize.cpp:147:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 147 | numNonCandRings < numAtomRings) { + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o -MF CMakeFiles/GraphMol.dir/Chirality.cpp.o.d -o CMakeFiles/GraphMol.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Chirality.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o @@ -3330,31 +3303,12 @@ cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o -MF CMakeFiles/GraphMol.dir/Conformer.cpp.o.d -o CMakeFiles/GraphMol.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o -MF CMakeFiles/GraphMol.dir/Renumber.cpp.o.d -o CMakeFiles/GraphMol.dir/Renumber.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Renumber.cpp -[ 19%] Linking CXX executable pickersTestsCatch -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickersTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -o pickersTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSimDivPickers.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKithc.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -MF CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o.d -o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/AdjustQuery.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 19%] Built target pickersTestsCatch [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o -MF CMakeFiles/GraphMol.dir/Resonance.cpp.o.d -o CMakeFiles/GraphMol.dir/Resonance.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Resonance.cpp -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Kekulize.cpp: In function 'void RDKit::{anonymous}::markDbondCands(RDKit::RWMol&, const RDKit::INT_VECT&, boost::dynamic_bitset<>&, RDKit::INT_VECT&, RDKit::INT_VECT&)': -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Kekulize.cpp:147:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 147 | numNonCandRings < numAtomRings) { - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o -MF CMakeFiles/GraphMol.dir/StereoGroup.cpp.o.d -o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/StereoGroup.cpp -[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o -MF CMakeFiles/GraphMol.dir/new_canon.cpp.o.d -o CMakeFiles/GraphMol.dir/new_canon.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/new_canon.cpp -[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -MF CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstanceGroup.cpp -[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o -MF CMakeFiles/GraphMol.dir/FindStereo.cpp.o.d -o CMakeFiles/GraphMol.dir/FindStereo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FindStereo.cpp -[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -MF CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MonomerInfo.cpp -[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -MF CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o.d -o CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/NontetrahedralStereo.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3370,11 +3324,16 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 20%] Linking CXX shared module ../../../rdkit/rdBase.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 20%] Built target rdBase +[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o -MF CMakeFiles/GraphMol.dir/new_canon.cpp.o.d -o CMakeFiles/GraphMol.dir/new_canon.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/new_canon.cpp +[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -MF CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstanceGroup.cpp +[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o -MF CMakeFiles/GraphMol.dir/FindStereo.cpp.o.d -o CMakeFiles/GraphMol.dir/FindStereo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FindStereo.cpp +[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -MF CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MonomerInfo.cpp +[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -MF CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o.d -o CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/NontetrahedralStereo.cpp [ 20%] Linking CXX shared library ../../lib/libRDKitGraphMol.so cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/GraphMol.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGraphMol.so.1 -o ../../lib/libRDKitGraphMol.so.1.2022.09.3 CMakeFiles/GraphMol.dir/Atom.cpp.o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o CMakeFiles/GraphMol.dir/QueryBond.cpp.o CMakeFiles/GraphMol.dir/Bond.cpp.o CMakeFiles/GraphMol.dir/MolOps.cpp.o CMakeFiles/GraphMol.dir/FindRings.cpp.o CMakeFiles/GraphMol.dir/ROMol.cpp.o CMakeFiles/GraphMol.dir/RWMol.cpp.o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o CMakeFiles/GraphMol.dir/atomic_data.cpp.o CMakeFiles/GraphMol.dir/QueryOps.cpp.o CMakeFiles/GraphMol.dir/MolPickler.cpp.o CMakeFiles/GraphMol.dir/Canon.cpp.o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o CMakeFiles/GraphMol.dir/BondIterators.cpp.o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o CMakeFiles/GraphMol.dir/Kekulize.cpp.o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o CMakeFiles/GraphMol.dir/AddHs.cpp.o CMakeFiles/GraphMol.dir/Matrices.cpp.o CMakeFiles/GraphMol.dir/Chirality.cpp.o CMakeFiles/GraphMol.dir/RingInfo.cpp.o CMakeFiles/GraphMol.dir/Conformer.cpp.o CMakeFiles/GraphMol.dir/Renumber.cpp.o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o CMakeFiles/GraphMol.dir/Resonance.cpp.o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o CMakeFiles/GraphMol.dir/new_canon.cpp.o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o CMakeFiles/GraphMol.dir/FindStereo.cpp.o CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl @@ -3382,130 +3341,97 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 20%] Built target GraphMol make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend -make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend -make -f Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/depend -make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend -make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake --color= -make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend +make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.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/GenericGroups/CMakeFiles/GenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/depend +make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/DependInfo.cmake --color= -make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.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/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake --color= -make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake --color= -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-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build -make -f Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 20%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -MF CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o.d -o CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs/Subgraphs.cpp +make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' +[ 21%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolTransforms_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLTRANSFORMS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -MF CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o.d -o CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/MolTransforms.cpp +[ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o +[ 21%] Building CXX object Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGenericGroups_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERICGROUPS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -MF CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o.d -o CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/GenericGroups/GenericGroups.cpp +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesParse.cpp +[ 21%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_TRAJECTORY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTrajectory_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o -MF CMakeFiles/Trajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/Trajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/Trajectory.cpp +[ 21%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Subgraphs/SubgraphUtils.cpp +[ 21%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolTransforms.so.1 -o ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 21%] Built target MolTransforms +make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 21%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -MF CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o.d -o CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/GasteigerCharges.cpp +[ 21%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/GenericGroups.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGenericGroups.so.1 -o ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build +[ 21%] Built target GenericGroups +make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build +make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 21%] Building CXX object Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolTransforms_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -MF CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o.d -o CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp +[ 21%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTrajectory.so.1 -o ../../../lib/libRDKitTrajectory.so.1.2022.09.3 CMakeFiles/Trajectory.dir/Trajectory.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 21%] Built target Trajectory +make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build +make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 20%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_TRAJECTORY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTrajectory_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o -MF CMakeFiles/Trajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/Trajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/Trajectory.cpp -[ 20%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -[ 20%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -MF CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o.d -o CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs/Subgraphs.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesParse.cpp -[ 20%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -[ 20%] Building CXX object Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -[ 20%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -[ 21%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -[ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o +[ 21%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp +[ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesParseOps.cpp -[ 22%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -[ 22%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Subgraphs/SubgraphUtils.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGenericGroups_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERICGROUPS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -MF CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o.d -o CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/GenericGroups/GenericGroups.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -MF CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o.d -o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/MolCatalogParams.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesWrite.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolTransforms_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLTRANSFORMS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -MF CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o.d -o CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/MolTransforms.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o -MF CMakeFiles/SLNParse.dir/SLNParse.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNParse.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/SLNParse.cpp -[ 22%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o -[ 22%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o -MF CMakeFiles/rdqueries.dir/rdqueries.cpp.o.d -o CMakeFiles/rdqueries.dir/rdqueries.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdqueries.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -MF CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o.d -o CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/MolCatalogEntry.cpp -[ 22%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -[ 22%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -MF CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o.d -o CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp -[ 22%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -MF CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o.d -o CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/GasteigerCharges.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o -MF CMakeFiles/MolInterchange.dir/Parser.cpp.o.d -o CMakeFiles/MolInterchange.dir/Parser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange/Parser.cpp -[ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -MF CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o.d -o CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/CIPMol.cpp -[ 22%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -MF CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o.d -o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/GasteigerParams.cpp -[ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -MF CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/CIPLabeler.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 21%] Linking CXX static library librdkitCatch.a +[ 21%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkitCatch.dir/link.txt --verbose=1 +/usr/bin/ar qc librdkitCatch.a CMakeFiles/rdkitCatch.dir/catch_main.cpp.o In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3520,78 +3446,98 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdqueries.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 22%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp -[ 22%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2022.09.3 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2022.09.3 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so +[ 21%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -MF CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o.d -o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/GasteigerParams.cpp +/usr/bin/ranlib librdkitCatch.a make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 22%] Built target MolCatalog -[ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -MF CMakeFiles/CIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Mancude.cpp -[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -MF CMakeFiles/CIPLabeler.dir/Digraph.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Digraph.cpp -[ 24%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so +[ 21%] Built target rdkitCatch +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-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 21%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -MF CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o.d -o CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/MolCatalogEntry.cpp +[ 21%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Subgraphs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubgraphs.so.1 -o ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1 ../../../lib/libRDKitSubgraphs.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 21%] Built target Subgraphs +make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' +[ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -MF CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o.d -o CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/CIPMol.cpp +[ 22%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitPartialCharges.so.1 -o ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 24%] Built target PartialCharges -make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend +[ 22%] Built target PartialCharges +make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build +make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 24%] Building CXX object Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolCatalog_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp -[ 24%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTrajectory.so.1 -o ../../../lib/libRDKitTrajectory.so.1.2022.09.3 CMakeFiles/Trajectory.dir/Trajectory.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so -[ 24%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o -MF CMakeFiles/rdqueries.dir/Queries.cpp.o.d -o CMakeFiles/rdqueries.dir/Queries.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Queries.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so +[ 22%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o -MF CMakeFiles/MolInterchange.dir/Parser.cpp.o.d -o CMakeFiles/MolInterchange.dir/Parser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange/Parser.cpp +[ 22%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitShapeHelpers.so.1 -o ../../../lib/libRDKitShapeHelpers.so.1.2022.09.3 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2022.09.3 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 24%] Built target Trajectory -make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend +[ 22%] Built target ShapeHelpers +make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build +make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 24%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -MF CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o.d -o CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer/BFGSOpt.cpp -[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o -MF CMakeFiles/CIPLabeler.dir/Node.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Node.cpp -[ 24%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Subgraphs.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubgraphs.so.1 -o ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1 ../../../lib/libRDKitSubgraphs.so +[ 22%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o -MF CMakeFiles/SLNParse.dir/SLNParse.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNParse.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/SLNParse.cpp +[ 23%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -MF CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o.d -o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/MolCatalogParams.cpp +[ 23%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend -[ 24%] Built target Subgraphs +[ 23%] Built target rdMolTransforms +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-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 23%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o -MF CMakeFiles/rdqueries.dir/rdqueries.cpp.o.d -o CMakeFiles/rdqueries.dir/rdqueries.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdqueries.cpp +[ 23%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2022.09.3 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2022.09.3 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 23%] Built target MolCatalog make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 24%] Building CXX object Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -[ 24%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdPartialCharges_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -MF CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o.d -o CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp +[ 23%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Trajectory.cpp -[ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmartsWrite.cpp +[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -MF CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/CIPLabeler.cpp +[ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesWrite.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3606,42 +3552,40 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdqueries.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 24%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/Numerics/Optimizer/LinearSearch.cpp -[ 24%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/GenericGroups.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGenericGroups.so.1 -o ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 24%] Built target GenericGroups -make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -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-202209.3/obj-i686-linux-gnu' -[ 25%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Substruct/SubstructMatch.cpp -[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/CIPLabeler/Edge.cpp -[ 25%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolTransforms.so.1 -o ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 25%] Built target MolTransforms -make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 25%] Building CXX object Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolTransforms_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -MF CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o.d -o CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp +[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -MF CMakeFiles/CIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Mancude.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Trajectory.cpp:11: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 23%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o -MF CMakeFiles/rdqueries.dir/Queries.cpp.o.d -o CMakeFiles/rdqueries.dir/Queries.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Queries.cpp +[ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmartsWrite.cpp +[ 23%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -MF CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/SLNAttribs.cpp +[ 23%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdTrajectory.cpp +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -MF CMakeFiles/CIPLabeler.dir/Digraph.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Digraph.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3660,8 +3604,8 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o -MF CMakeFiles/CIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Sort.cpp +[ 24%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolInterchange/Writer.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3672,18 +3616,62 @@ from /usr/include/boost/smart_ptr.hpp:19, from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.h:15, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp:5: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdTrajectory.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 25%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o +[ 24%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdtrajectory.so CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 24%] Built target rdtrajectory +make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 24%] Building CXX object Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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 CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/catch_tests.cpp +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o -MF CMakeFiles/CIPLabeler.dir/Node.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Node.cpp +[ 24%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o -MF CMakeFiles/SLNParse.dir/sln.tab.cpp.o.d -o CMakeFiles/SLNParse.dir/sln.tab.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/sln.tab.cpp +[ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/SmilesParse/CXSmilesOps.cpp -[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/CIPLabeler/configs/Configuration.cpp +[ 24%] Linking CXX executable pickersTestsCatch +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickersTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -o pickersTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSimDivPickers.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKithc.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 24%] Built target pickersTestsCatch +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-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' +[ 24%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -MF CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o.d -o CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp +[ 24%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdqueries.so CMakeFiles/rdqueries.dir/rdqueries.cpp.o CMakeFiles/rdqueries.dir/Queries.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 24%] Built target rdqueries +make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +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-202209.3/obj-i686-linux-gnu' +[ 25%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Substruct/SubstructMatch.cpp +[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/CIPLabeler/Edge.cpp +[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o -MF CMakeFiles/CIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Sort.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3691,17 +3679,36 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp:11: + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/CIPLabeler/configs/Configuration.cpp +[ 25%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInterchange.so.1 -o ../../../lib/libRDKitMolInterchange.so.1.2022.09.3 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so +[ 25%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2022.09.3 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 25%] Built target MolInterchange +make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 25%] Building CXX object Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/dictTestsCatch.dir/catch_dict.cpp.o -MF CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o.d -o CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/catch_dict.cpp +[ 25%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -MF CMakeFiles/SLNParse.dir/lex.yysln.cpp.o.d -o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/lex.yysln.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3716,52 +3723,133 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Trajectory.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 25%] Linking CXX executable dictTestsCatch +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/dictTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -o dictTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl [ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp -[ 25%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/Optimizer.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2022.09.3 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1 ../../../lib/libRDKitOptimizer.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 25%] Built target Optimizer -make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend +[ 25%] Built target dictTestsCatch +make -f Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/logTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/logTestsCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build +make -f Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 25%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp -[ 25%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp -[ 25%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/smarts.tab.cpp -[ 25%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -MF CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/SLNAttribs.cpp +[ 25%] Building CXX object Code/RDGeneral/CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/RDGeneral/catch_logs.cpp +[ 25%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/SubstructUtils.cpp +[ 25%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2022.09.3 CMakeFiles/SLNParse.dir/SLNParse.cpp.o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o CMakeFiles/SLNParse.dir/sln.tab.cpp.o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2022.09.3 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so +[ 25%] Linking CXX executable logTestsCatch +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/logTestsCatch.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -o logTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 25%] Built target SLNParse +make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Geometry /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' +[ 25%] Building CXX object Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/Geometry/catch_tests.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 25%] Built target logTestsCatch +make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 25%] Building CXX object Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o -MF CMakeFiles/testConrec.dir/testConrec.cpp.o.d -o CMakeFiles/testConrec.dir/testConrec.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/testConrec.cpp [ 25%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdChemicalFeatures.so CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../../lib/libRDKitChemicalFeatures.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 25%] Built target rdChemicalFeatures -[ 25%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o -MF CMakeFiles/SLNParse.dir/sln.tab.cpp.o.d -o CMakeFiles/SLNParse.dir/sln.tab.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/sln.tab.cpp -[ 25%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdPartialCharges.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdPartialCharges.so CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 25%] Built target rdPartialCharges -make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend +make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake --color= +[ 25%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -MF CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o.d -o CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer/BFGSOpt.cpp +[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.h:24, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:25, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/SubstructUtils.cpp:13: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 25%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/Numerics/Optimizer/LinearSearch.cpp +[ 25%] Linking CXX executable testConrec +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConrec.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testConrec.dir/testConrec.cpp.o -o testConrec ../RDGeneral/librdkitCatch.a ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build +[ 25%] Built target testConrec +make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 25%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -MF CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o.d -o CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer/testOptimizer.cpp +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 25%] Building CXX object Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdPartialCharges_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -MF CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o.d -o CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp +[ 25%] Linking CXX executable geometryTestsCatch +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/geometryTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -o geometryTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 25%] Built target geometryTestsCatch +make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 25%] Building CXX object Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -MF CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o.d -o CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp +[ 25%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/Optimizer.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2022.09.3 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1 ../../../lib/libRDKitOptimizer.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 25%] Built target Optimizer +make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 25%] Building CXX object Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolCatalog_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp +[ 25%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/smarts.tab.cpp +[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3776,98 +3864,26 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 25%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolInterchange/Writer.cpp -[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp -make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ForceField /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 25%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o -MF CMakeFiles/ForceField.dir/ForceField.cpp.o.d -o CMakeFiles/ForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/ForceField.cpp -[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp -[ 25%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitShapeHelpers.so.1 -o ../../../lib/libRDKitShapeHelpers.so.1.2022.09.3 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 25%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdTrajectory.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2022.09.3 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 25%] Built target ShapeHelpers -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp [ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule2.cpp -[ 26%] Linking CXX executable testOptimizer -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/testOptimizer.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -o testOptimizer ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 26%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -[ 26%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/smiles.tab.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o ../../../../lib/libRDKitMolCatalog.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 26%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructMatch.so.1 -o ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 26%] Built target testOptimizer -make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend +[ 26%] Built target SubstructMatch +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-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build +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-202209.3/obj-i686-linux-gnu' -[ 26%] Building CXX object Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -MF CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o.d -o CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 26%] Built target rdMolCatalog -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/CIPLabeler/rules/Rule3.cpp -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/CIPLabeler/rules/Rule5.cpp -[ 26%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/SubstructUtils.cpp -In file included from /build/reproducible-path/rdkit-202209.3/Code/ForceField/ForceField.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/ForceField/ForceField.cpp:11: -In copy constructor 'RDKit::Snapshot::Snapshot(const RDKit::Snapshot&)', - inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = RDKit::Snapshot; _Args = {const RDKit::Snapshot&}; _Tp = RDKit::Snapshot]' at /usr/include/c++/12/bits/new_allocator.h:175:4, - inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = RDKit::Snapshot; _Args = {const RDKit::Snapshot&}; _Tp = RDKit::Snapshot]' at /usr/include/c++/12/bits/alloc_traits.h:516:17, - inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1281:30, - inlined from 'int BFGSOpt::minimize(unsigned int, double*, double, unsigned int&, double&, EnergyFunctor, GradientFunctor, unsigned int, RDKit::SnapshotVect*, double, unsigned int) [with EnergyFunctor = ForceFieldsHelper::calcEnergy; GradientFunctor = ForceFieldsHelper::calcGradient]' at /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer/BFGSOpt.h:261:32, - inlined from 'int ForceFields::ForceField::minimize(unsigned int, RDKit::SnapshotVect*, unsigned int, double, double)' at /build/reproducible-path/rdkit-202209.3/Code/ForceField/ForceField.cpp:289:24: -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/Snapshot.h:26:31: warning: 'finalForce' may be used uninitialized [-Wmaybe-uninitialized] - 26 | class RDKIT_TRAJECTORY_EXPORT Snapshot { - | ^~~~~~~~ -/build/reproducible-path/rdkit-202209.3/Code/ForceField/ForceField.cpp: In member function 'int ForceFields::ForceField::minimize(unsigned int, RDKit::SnapshotVect*, unsigned int, double, double)': -/build/reproducible-path/rdkit-202209.3/Code/ForceField/ForceField.cpp:281:10: note: 'finalForce' was declared here - 281 | double finalForce; - | ^~~~~~~~~~ -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp -[ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/ForceField/UFF/AngleBend.cpp -[ 27%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/lex.yysmarts.cpp -[ 27%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -MF CMakeFiles/SLNParse.dir/lex.yysln.cpp.o.d -o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/lex.yysln.cpp -[ 27%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 27%] Built target rdMolTransforms -[ 28%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/lex.yysmiles.cpp +[ 26%] Building CXX object Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolInterchange_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3886,8 +3902,9 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule6.cpp +[ 26%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdPartialCharges.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdPartialCharges.so CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3898,37 +3915,28 @@ from /usr/include/boost/smart_ptr.hpp:19, from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdTrajectory.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.h:15, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp:5: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp -[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/BondStretch.cpp -[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/Nonbonded.cpp -[ 29%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdqueries.so CMakeFiles/rdqueries.dir/rdqueries.cpp.o CMakeFiles/rdqueries.dir/Queries.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/ForceField/UFF/Inversion.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 29%] Built target rdqueries -[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -MF CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/TorsionAngle.cpp -[ 29%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdtrajectory.so CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so -[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/DistanceConstraint.cpp +[ 26%] Built target rdPartialCharges +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-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 29%] Built target rdtrajectory -[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/AngleConstraint.cpp +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-202209.3/obj-i686-linux-gnu' +[ 26%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/CIPLabeler/rules/Rule3.cpp +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3936,146 +3944,276 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.h:24, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:25, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/SubstructUtils.cpp:13: + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp:35: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 26%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/smiles.tab.cpp +[ 26%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdShapeHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdShapeHelpers.so CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o ../../../../lib/libRDKitShapeHelpers.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 26%] Built target rdShapeHelpers +make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 26%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -MF CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o.d -o CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer/testOptimizer.cpp +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp +[ 26%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o ../../../../lib/libRDKitMolCatalog.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 26%] Built target rdMolCatalog +make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ForceField /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o -MF CMakeFiles/ForceField.dir/ForceField.cpp.o.d -o CMakeFiles/ForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/ForceField.cpp +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/CIPLabeler/rules/Rule5.cpp +[ 26%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolInterchange.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolInterchange.so CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o ../../../../lib/libRDKitMolInterchange.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 26%] Built target rdMolInterchange +[ 26%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSLNParse.dir/link.txt --verbose=1 +[ 26%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/lex.yysmarts.cpp +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o ../../../../lib/libRDKitSLNParse.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 26%] Built target rdSLNParse +[ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/ForceField/UFF/AngleBend.cpp +[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp +[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule6.cpp +[ 27%] Linking CXX executable testOptimizer +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/testOptimizer.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -o testOptimizer ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 27%] Built target testOptimizer +[ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/BondStretch.cpp +[ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/Nonbonded.cpp +[ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp +In file included from /build/reproducible-path/rdkit-202209.3/Code/ForceField/ForceField.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/ForceField/ForceField.cpp:11: +In copy constructor 'RDKit::Snapshot::Snapshot(const RDKit::Snapshot&)', + inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = RDKit::Snapshot; _Args = {const RDKit::Snapshot&}; _Tp = RDKit::Snapshot]' at /usr/include/c++/12/bits/new_allocator.h:175:4, + inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = RDKit::Snapshot; _Args = {const RDKit::Snapshot&}; _Tp = RDKit::Snapshot]' at /usr/include/c++/12/bits/alloc_traits.h:516:17, + inlined from 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1281:30, + inlined from 'int BFGSOpt::minimize(unsigned int, double*, double, unsigned int&, double&, EnergyFunctor, GradientFunctor, unsigned int, RDKit::SnapshotVect*, double, unsigned int) [with EnergyFunctor = ForceFieldsHelper::calcEnergy; GradientFunctor = ForceFieldsHelper::calcGradient]' at /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer/BFGSOpt.h:261:32, + inlined from 'int ForceFields::ForceField::minimize(unsigned int, RDKit::SnapshotVect*, unsigned int, double, double)' at /build/reproducible-path/rdkit-202209.3/Code/ForceField/ForceField.cpp:289:24: +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/Snapshot.h:26:31: warning: 'finalForce' may be used uninitialized [-Wmaybe-uninitialized] + 26 | class RDKIT_TRAJECTORY_EXPORT Snapshot { + | ^~~~~~~~ +/build/reproducible-path/rdkit-202209.3/Code/ForceField/ForceField.cpp: In member function 'int ForceFields::ForceField::minimize(unsigned int, RDKit::SnapshotVect*, unsigned int, double, double)': +/build/reproducible-path/rdkit-202209.3/Code/ForceField/ForceField.cpp:281:10: note: 'finalForce' was declared here + 281 | double finalForce; + | ^~~~~~~~~~ +[ 29%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/lex.yysmiles.cpp +[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/ForceField/UFF/Inversion.cpp +[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -MF CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/TorsionAngle.cpp +[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/DistanceConstraint.cpp +[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/AngleConstraint.cpp [ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/TorsionConstraint.cpp +[ 29%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/CIPLabeler.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCIPLabeler.so.1 -o ../../../lib/libRDKitCIPLabeler.so.1.2022.09.3 CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o CMakeFiles/CIPLabeler.dir/Node.cpp.o CMakeFiles/CIPLabeler.dir/Edge.cpp.o CMakeFiles/CIPLabeler.dir/Sort.cpp.o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitCIPLabeler.so.1.2022.09.3 ../../../lib/libRDKitCIPLabeler.so.1 ../../../lib/libRDKitCIPLabeler.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 29%] Built target CIPLabeler [ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/PositionConstraint.cpp [ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/ForceField/UFF/Params.cpp -[ 30%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInterchange.so.1 -o ../../../lib/libRDKitMolInterchange.so.1.2022.09.3 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so [ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/AngleBend.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2022.09.3 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 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-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' -[ 30%] Building CXX object Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolInterchange_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp [ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/BondStretch.cpp +[ 30%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so [ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/StretchBend.cpp +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 30%] Built target SmilesParse +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-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 30%] Building CXX object Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdCIPLabeler_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -MF CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o.d -o CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Wrap/rdCIPLabeler.cpp [ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/OopBend.cpp -[ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/ForceField/MMFF/TorsionAngle.cpp -[ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/Nonbonded.cpp -[ 30%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2022.09.3 CMakeFiles/SLNParse.dir/SLNParse.cpp.o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o CMakeFiles/SLNParse.dir/sln.tab.cpp.o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2022.09.3 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so +[ 30%] Linking CXX shared module ../../../rdkit/rdBase.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 30%] Built target SLNParse -make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend +[ 30%] Built target rdBase +make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build +make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 30%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp +[ 30%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_REDUCEDGRAPHS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DReducedGraphs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -MF CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o.d -o CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp +[ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/ForceField/MMFF/TorsionAngle.cpp +[ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/Nonbonded.cpp [ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/DistanceConstraint.cpp -[ 30%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/CIPLabeler.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCIPLabeler.so.1 -o ../../../lib/libRDKitCIPLabeler.so.1.2022.09.3 CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o CMakeFiles/CIPLabeler.dir/Node.cpp.o CMakeFiles/CIPLabeler.dir/Edge.cpp.o CMakeFiles/CIPLabeler.dir/Sort.cpp.o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so [ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/AngleConstraint.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitCIPLabeler.so.1.2022.09.3 ../../../lib/libRDKitCIPLabeler.so.1 ../../../lib/libRDKitCIPLabeler.so +[ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/TorsionConstraint.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Wrap/rdCIPLabeler.cpp:13: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/PositionConstraint.cpp +[ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/Params.cpp +[ 31%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCIPLabeler.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdCIPLabeler.so CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o ../../../../lib/libRDKitCIPLabeler.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 31%] Built target CIPLabeler -make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/depend +[ 31%] Built target rdCIPLabeler +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-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build +make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 31%] Building CXX object Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdCIPLabeler_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -MF CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o.d -o CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Wrap/rdCIPLabeler.cpp -[ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/TorsionConstraint.cpp -[ 31%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdShapeHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdShapeHelpers.so CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o ../../../../lib/libRDKitShapeHelpers.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 31%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o -MF CMakeFiles/testSLNParse.dir/test.cpp.o.d -o CMakeFiles/testSLNParse.dir/test.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/test.cpp +[ 31%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitReducedGraphs.so.1 -o ../../../lib/libRDKitReducedGraphs.so.1.2022.09.3 CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitReducedGraphs.so.1.2022.09.3 ../../../lib/libRDKitReducedGraphs.so.1 ../../../lib/libRDKitReducedGraphs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 31%] Built target rdShapeHelpers -[ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/PositionConstraint.cpp -[ 31%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so -[ 31%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructMatch.so.1 -o ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so +[ 31%] Built target ReducedGraphs +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-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 31%] Built target SubstructMatch +make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 31%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ABBREVIATIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -MF CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o.d -o CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/Abbreviations.cpp +[ 31%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ABBREVIATIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -MF CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o.d -o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp +[ 31%] Linking CXX shared library ../../lib/libRDKitForceField.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2022.09.3 CMakeFiles/ForceField.dir/ForceField.cpp.o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/Params.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o ../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2022.09.3 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/Params.cpp -[ 31%] Built target SmilesParse +[ 31%] Built target ForceField make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend +make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend +make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend +make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 31%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolAlign/AlignMolecules.cpp -make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 31%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o +[ 31%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o +[ 31%] Building CXX object Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -MF CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o.d -o CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms/ChemTransforms.cpp +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp +[ 31%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/graphmolcpTest.dir/cptest.cpp.o -MF CMakeFiles/graphmolcpTest.dir/cptest.cpp.o.d -o CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/cptest.cpp +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolAlign/AlignMolecules.cpp [ 32%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -MF CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o.d -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms/MolFragmenter.cpp -make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake --color= +[ 32%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/Abbreviations.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAbbreviations.so.1 -o ../../../lib/libRDKitAbbreviations.so.1.2022.09.3 CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAbbreviations.so.1.2022.09.3 ../../../lib/libRDKitAbbreviations.so.1 ../../../lib/libRDKitAbbreviations.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 32%] Building CXX object Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/graphmolcpTest.dir/cptest.cpp.o -MF CMakeFiles/graphmolcpTest.dir/cptest.cpp.o.d -o CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/cptest.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp:10: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ +[ 32%] Built target Abbreviations make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/DependInfo.cmake --color= @@ -4084,6 +4222,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 32%] Building CXX object Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/GraphMol/querytest.cpp +[ 32%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/ForceFieldHelpers/UFF/Builder.cpp +[ 32%] Linking CXX executable graphmolcpTest +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolcpTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -o graphmolcpTest ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 32%] Built target graphmolcpTest make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake --color= @@ -4092,6 +4237,12 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 33%] Building CXX object Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/graphmolIterTest.dir/itertest.cpp.o -MF CMakeFiles/graphmolIterTest.dir/itertest.cpp.o.d -o CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/itertest.cpp +[ 33%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolAlign.so.1 -o ../../../lib/libRDKitMolAlign.so.1.2022.09.3 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 33%] Built target MolAlign make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake --color= @@ -4100,6 +4251,15 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 33%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/graphmolMemTest1.dir/memtest1.cpp.o -MF CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o.d -o CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/memtest1.cpp +[ 33%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp +[ 33%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp +[ 33%] Linking CXX executable graphmolqueryTest +cd /build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -o graphmolqueryTest ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 33%] Built target graphmolqueryTest 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake --color= @@ -4108,24 +4268,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 33%] Building CXX object Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/test-valgrind.dir/test-valgrind.cpp.o -MF CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o.d -o CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/test-valgrind.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp:35: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ +[ 33%] Linking CXX executable testSLNParse +cd /build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSLNParse.dir/test.cpp.o -o testSLNParse ../../../lib/libRDKitSLNParse.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 33%] Built target testSLNParse make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/DependInfo.cmake --color= @@ -4134,6 +4281,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 33%] Building CXX object Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -MF CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o.d -o CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/catch_moliterators.cpp +[ 33%] Linking CXX executable graphmolIterTest +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolIterTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -o graphmolIterTest ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 33%] Built target graphmolIterTest 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake --color= @@ -4142,6 +4294,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 33%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o -MF CMakeFiles/smiTest2.dir/test2.cpp.o.d -o CMakeFiles/smiTest2.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/test2.cpp +[ 33%] Linking CXX executable graphmolMemTest1 +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMemTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -o graphmolMemTest1 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 33%] Built target graphmolMemTest1 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/DependInfo.cmake --color= @@ -4150,23 +4307,12 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 33%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o -MF CMakeFiles/smaTest1.dir/smatest.cpp.o.d -o CMakeFiles/smaTest1.dir/smatest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/smatest.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Wrap/rdCIPLabeler.cpp:13: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 33%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemTransforms.so.1 -o ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1 ../../../lib/libRDKitChemTransforms.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 33%] Built target ChemTransforms 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/DependInfo.cmake --color= @@ -4175,11 +4321,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 33%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Fingerprints.cpp -[ 33%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolInterchange.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolInterchange.so CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o ../../../../lib/libRDKitMolInterchange.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 33%] Linking CXX executable smiTest2 +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTest2.dir/test2.cpp.o -o smiTest2 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 33%] Built target rdMolInterchange +[ 33%] Built target smiTest2 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake --color= @@ -4188,11 +4334,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 33%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o -MF CMakeFiles/FilterCatalog.dir/Filters.cpp.o.d -o CMakeFiles/FilterCatalog.dir/Filters.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Filters.cpp -[ 33%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSLNParse.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o ../../../../lib/libRDKitSLNParse.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 33%] Linking CXX executable test-valgrind +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-valgrind.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o" -o test-valgrind ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 33%] Built target rdSLNParse +[ 33%] Built target test-valgrind 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake --color= @@ -4204,11 +4350,8 @@ [ 33%] Linking CXX executable moliteratorTestsCatch cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/moliteratorTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -o moliteratorTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 33%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCIPLabeler.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdCIPLabeler.so CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o ../../../../lib/libRDKitCIPLabeler.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 33%] Built target rdCIPLabeler +[ 33%] Built target moliteratorTestsCatch 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/DependInfo.cmake --color= @@ -4217,181 +4360,119 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 33%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/GraphMol/Subgraphs/test2.cpp +[ 34%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.cpp +[ 34%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp +[ 34%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FilterCatalog/FilterCatalog.cpp +[ 34%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/PatternFingerprints.cpp +[ 34%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganFingerprints.cpp +[ 35%] Linking CXX executable testSubgraphs1 +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSubgraphs1.dir/test1.cpp.o -o testSubgraphs1 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 33%] Built target moliteratorTestsCatch +[ 35%] Built target testSubgraphs1 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 33%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o +[ 35%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp -[ 33%] Linking CXX executable graphmolMemTest1 -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMemTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -o graphmolMemTest1 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 35%] Linking CXX executable testSubgraphs2 +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSubgraphs2.dir/test2.cpp.o -o testSubgraphs2 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 33%] Built target graphmolMemTest1 +[ 35%] Built target testSubgraphs2 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 33%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o +[ 35%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/GraphMol/PartialCharges/test1.cpp -[ 33%] Linking CXX executable test-valgrind -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-valgrind.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o" -o test-valgrind ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 35%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceFieldHelpers.so.1 -o ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 33%] Built target test-valgrind +[ 35%] Built target ForceFieldHelpers make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 33%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o +[ 35%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp -[ 33%] Linking CXX executable smiTest2 -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest2.dir/link.txt --verbose=1 -[ 33%] Linking CXX executable graphmolcpTest -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolcpTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTest2.dir/test2.cpp.o -o smiTest2 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -o graphmolcpTest ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 33%] Built target smiTest2 +[ 35%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairs.cpp +[ 36%] Linking CXX executable testPartialCharges +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPartialCharges.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testPartialCharges.dir/test1.cpp.o -o testPartialCharges ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 36%] Built target testPartialCharges make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/DependInfo.cmake --color= -[ 33%] Built target graphmolcpTest -make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build -[ 33%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o +[ 36%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o -MF CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/catch_tests.cpp -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 33%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_REDUCEDGRAPHS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DReducedGraphs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -MF CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o.d -o CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp -[ 33%] Linking CXX shared library ../../lib/libRDKitForceField.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2022.09.3 CMakeFiles/ForceField.dir/ForceField.cpp.o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/Params.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o ../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 33%] Linking CXX executable graphmolIterTest -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolIterTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -o graphmolIterTest ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2022.09.3 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 33%] Built target graphmolIterTest -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-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/DependInfo.cmake --color= -[ 33%] Built target ForceField -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-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 33%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o -MF CMakeFiles/testSLNParse.dir/test.cpp.o.d -o CMakeFiles/testSLNParse.dir/test.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/test.cpp -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 33%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ABBREVIATIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -MF CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o.d -o CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/Abbreviations.cpp -[ 33%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolAlign.so.1 -o ../../../lib/libRDKitMolAlign.so.1.2022.09.3 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 33%] Built target MolAlign -make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 34%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o -MF CMakeFiles/Depictor.dir/RDDepictor.cpp.o.d -o CMakeFiles/Depictor.dir/RDDepictor.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/RDDepictor.cpp -[ 34%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FilterCatalog/FilterCatalog.cpp -[ 34%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/PatternFingerprints.cpp -[ 34%] Linking CXX executable testSubgraphs2 -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSubgraphs2.dir/test2.cpp.o -o testSubgraphs2 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 34%] Built target testSubgraphs2 -[ 34%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ABBREVIATIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -MF CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o.d -o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp -[ 35%] Linking CXX executable testPartialCharges -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPartialCharges.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testPartialCharges.dir/test1.cpp.o -o testPartialCharges ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 35%] Built target testPartialCharges -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-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/External/CoordGen/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/CoordGen/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 35%] Building CXX object External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/CoordGen/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdCoordGen_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -MF CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o.d -o CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -c /build/reproducible-path/rdkit-202209.3/External/CoordGen/Wrap/rdCoordGen.cpp -[ 35%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o +[ 36%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.cpp -[ 35%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/CIPMol.cpp -[ 35%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o +[ 36%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatGenerator.cpp -[ 35%] Linking CXX executable graphmolqueryTest -cd /build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -o graphmolqueryTest ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o -MF CMakeFiles/Fingerprints.dir/MACCS.cpp.o.d -o CMakeFiles/Fingerprints.dir/MACCS.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MACCS.cpp +[ 36%] Linking CXX executable smaTest1 +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smaTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smaTest1.dir/smatest.cpp.o -o smaTest1 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 35%] Built target graphmolqueryTest -make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend +[ 36%] Built target smaTest1 +make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.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-202209.3/obj-i686-linux-gnu' -[ 35%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp -[ 35%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemTransforms.so.1 -o ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1 ../../../lib/libRDKitChemTransforms.so +[ 36%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o -MF CMakeFiles/testReducedGraphs.dir/test1.cpp.o.d -o CMakeFiles/testReducedGraphs.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/test1.cpp +[ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o -MF CMakeFiles/Fingerprints.dir/MHFP.cpp.o.d -o CMakeFiles/Fingerprints.dir/MHFP.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MHFP.cpp +[ 36%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp +[ 36%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp +[ 36%] Linking CXX executable testReducedGraphs +cd /build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testReducedGraphs.dir/test1.cpp.o -o testReducedGraphs ../../../lib/libRDKitReducedGraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 36%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 35%] Built target ChemTransforms -make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend +[ 36%] Built target testReducedGraphs +make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build +make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 35%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/rdchem.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/rdchem.cpp.o -MF CMakeFiles/rdchem.dir/rdchem.cpp.o.d -o CMakeFiles/rdchem.dir/rdchem.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdchem.cpp -[ 35%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitReducedGraphs.so.1 -o ../../../lib/libRDKitReducedGraphs.so.1.2022.09.3 CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 36%] Linking CXX executable testSubgraphs1 -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSubgraphs1.dir/test1.cpp.o -o testSubgraphs1 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitReducedGraphs.so.1.2022.09.3 ../../../lib/libRDKitReducedGraphs.so.1 ../../../lib/libRDKitReducedGraphs.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 36%] Built target ReducedGraphs -[ 36%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/ForceFieldHelpers/UFF/Builder.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 36%] Built target testSubgraphs1 -[ 36%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp +[ 37%] Building CXX object Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdReducedGraphs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp +[ 38%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp +[ 38%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp +[ 38%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp +[ 38%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/CIPMol.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4406,38 +4487,71 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/External/CoordGen/Wrap/rdCoordGen.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp:13: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 36%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatParams.cpp -[ 36%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp -[ 36%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o +[ 38%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/CIPLabeler.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/CIPLabeler.cpp -[ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganFingerprints.cpp -[ 36%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/Abbreviations.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAbbreviations.so.1 -o ../../../lib/libRDKitAbbreviations.so.1.2022.09.3 CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAbbreviations.so.1.2022.09.3 ../../../lib/libRDKitAbbreviations.so.1 ../../../lib/libRDKitAbbreviations.so +[ 38%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdReducedGraphs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdReducedGraphs.so CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o ../../../../lib/libRDKitReducedGraphs.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 36%] Built target Abbreviations -make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/depend +[ 38%] Built target rdReducedGraphs +[ 38%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp +[ 38%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Mancude.cpp +[ 38%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatParams.cpp +[ 38%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp +[ 38%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalogRunner.cpp +[ 38%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolChemicalFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o ../../../lib/libRDKitMolChemicalFeatures.so.1.2022.09.3 CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2022.09.3 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 38%] Built target MolChemicalFeatures +[ 39%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatchers.cpp +[ 39%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Digraph.cpp +[ 40%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Node.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Node.cpp +[ 40%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Edge.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Edge.cpp +[ 41%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2022.09.3 CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2022.09.3 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 41%] Built target FragCatalog +make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build +make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 36%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o -MF CMakeFiles/testReducedGraphs.dir/test1.cpp.o.d -o CMakeFiles/testReducedGraphs.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/test1.cpp -[ 36%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Mancude.cpp -[ 36%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Depictor/EmbeddedFrag.cpp -[ 36%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp +[ 41%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/rdchem.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/rdchem.cpp.o -MF CMakeFiles/rdchem.dir/rdchem.cpp.o.d -o CMakeFiles/rdchem.dir/rdchem.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdchem.cpp +[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/Sort.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Sort.cpp +[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Configuration.cpp +[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp +[ 41%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -MF CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp +[ 41%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp +[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp +[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp +[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4455,67 +4569,46 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 36%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp -[ 36%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp -[ 36%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp -[ 36%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o -MF CMakeFiles/Depictor.dir/DepictUtils.cpp.o.d -o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/DepictUtils.cpp -[ 36%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/CoordGen/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdCoordGen.so CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so -[ 37%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 37%] Built target rdCoordGen -make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 38%] Building CXX object Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdReducedGraphs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp -[ 38%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Digraph.cpp -[ 38%] Linking CXX executable testReducedGraphs -cd /build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testReducedGraphs.dir/test1.cpp.o -o testReducedGraphs ../../../lib/libRDKitReducedGraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule2.cpp +[ 42%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule3.cpp +[ 42%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp +[ 42%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp +[ 42%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/Rule4c.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp +[ 42%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/Rule5.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule5.cpp +[ 42%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so +[ 42%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/Rule5New.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 38%] Built target testReducedGraphs +[ 42%] Built target FilterCatalog make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 38%] Building CXX object Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o +[ 42%] Building CXX object Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdAbbreviations_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp -[ 39%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Node.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Node.cpp -[ 39%] Linking CXX executable smaTest1 -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smaTest1.dir/link.txt --verbose=1 -[ 39%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smaTest1.dir/smatest.cpp.o -o smaTest1 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 39%] Built target smaTest1 -[ 39%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalogRunner.cpp -[ 39%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairs.cpp -[ 40%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2022.09.3 CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2022.09.3 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 40%] Built target FragCatalog -[ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o -MF CMakeFiles/Fingerprints.dir/MACCS.cpp.o.d -o CMakeFiles/Fingerprints.dir/MACCS.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MACCS.cpp -[ 40%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp +[ 42%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/Rule6.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule6.cpp +[ 42%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintUtil.cpp +[ 42%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/SequenceRule.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp +[ 42%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp +[ 42%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o -MF CMakeFiles/rdchem.dir/Table.cpp.o.d -o CMakeFiles/rdchem.dir/Table.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Table.cpp +[ 42%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o -MF CMakeFiles/rdchem.dir/Atom.cpp.o.d -o CMakeFiles/rdchem.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Atom.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4530,7 +4623,7 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp:13: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -4548,92 +4641,13 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Atom.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o -MF CMakeFiles/Fingerprints.dir/MHFP.cpp.o.d -o CMakeFiles/Fingerprints.dir/MHFP.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MHFP.cpp -[ 40%] Linking CXX executable testSLNParse -cd /build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSLNParse.dir/test.cpp.o -o testSLNParse ../../../lib/libRDKitSLNParse.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 40%] Built target testSLNParse -[ 41%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp -[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Edge.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Edge.cpp -[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/Sort.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Sort.cpp -[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Configuration.cpp -[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp -[ 41%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp -[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdReducedGraphs.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdReducedGraphs.so CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o ../../../../lib/libRDKitReducedGraphs.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 41%] Built target rdReducedGraphs -[ 41%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp -[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp -[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp -[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp -[ 41%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolChemicalFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o ../../../lib/libRDKitMolChemicalFeatures.so.1.2022.09.3 CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2022.09.3 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so -[ 41%] Linking CXX shared library ../../../lib/libRDKitDepictor.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/Depictor.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDepictor.so.1 -o ../../../lib/libRDKitDepictor.so.1.2022.09.3 CMakeFiles/Depictor.dir/RDDepictor.cpp.o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o CMakeFiles/Depictor.dir/DepictUtils.cpp.o ../../../lib/libRDKitMolAlign.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 41%] Built target MolChemicalFeatures -[ 41%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o -MF CMakeFiles/rdchem.dir/Table.cpp.o.d -o CMakeFiles/rdchem.dir/Table.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Table.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 41%] Built target Depictor -[ 41%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp -[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule2.cpp -[ 42%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatchers.cpp -[ 42%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceFieldHelpers.so.1 -o ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 42%] Built target ForceFieldHelpers -make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 42%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp -[ 42%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp -[ 42%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o -MF CMakeFiles/rdchem.dir/Atom.cpp.o.d -o CMakeFiles/rdchem.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Atom.cpp -[ 43%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule3.cpp -[ 43%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintUtil.cpp -[ 43%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp -[ 43%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp -[ 43%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp -[ 43%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/Rule4c.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp +[ 43%] Linking CXX executable testCIPLabeler +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCIPLabeler.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o CMakeFiles/testCIPLabeler.dir/Node.cpp.o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -o testCIPLabeler ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4652,35 +4666,34 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 43%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/Rule5.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule5.cpp -[ 43%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/Rule5New.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp -[ 43%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/Rule6.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule6.cpp -[ 43%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/SequenceRule.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp -[ 43%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 43%] Built target testCIPLabeler +make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 44%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o -MF CMakeFiles/Depictor.dir/RDDepictor.cpp.o.d -o CMakeFiles/Depictor.dir/RDDepictor.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/RDDepictor.cpp +[ 44%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o -MF CMakeFiles/rdchem.dir/Bond.cpp.o.d -o CMakeFiles/rdchem.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Bond.cpp -[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAbbreviations.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdAbbreviations.so CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o ../../../../lib/libRDKitAbbreviations.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 44%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o -MF CMakeFiles/rdchem.dir/Mol.cpp.o.d -o CMakeFiles/rdchem.dir/Mol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Mol.cpp +[ 44%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2022.09.3 CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o CMakeFiles/Fingerprints.dir/MACCS.cpp.o CMakeFiles/Fingerprints.dir/MHFP.cpp.o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 44%] Built target rdAbbreviations -make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend +[ 44%] Built target Fingerprints +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-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/External/CoordGen/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/CoordGen/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build +make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FileParsers/CDXMLParser.cpp -[ 44%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -MF CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp -[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FileParsers/Mol2FileParser.cpp +[ 44%] Building CXX object External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/CoordGen/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdCoordGen_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -MF CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o.d -o CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -c /build/reproducible-path/rdkit-202209.3/External/CoordGen/Wrap/rdCoordGen.cpp +[ 44%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o -MF CMakeFiles/rdchem.dir/Mol.cpp.o.d -o CMakeFiles/rdchem.dir/Mol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Mol.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4695,12 +4708,12 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Bond.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FileParsers/MolFileParser.cpp +[ 44%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Wrap/Conformer.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4715,31 +4728,15 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Atom.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp:11: + from /build/reproducible-path/rdkit-202209.3/External/CoordGen/Wrap/rdCoordGen.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FileParsers/MolSGroupParsing.cpp -[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FileParsers/MolSGroupWriting.cpp +[ 45%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAbbreviations.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdAbbreviations.so CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o ../../../../lib/libRDKitAbbreviations.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 45%] Built target rdAbbreviations make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DistGeom /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake --color= @@ -4748,8 +4745,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 45%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -MF CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DistGeom/DistGeomUtils.cpp -[ 45%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -MF CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o.d -o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DistGeom/TriangleSmooth.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4764,7 +4759,7 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Bond.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Conformer.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -4786,44 +4781,19 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 45%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp -[ 46%] Linking CXX executable testCIPLabeler -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCIPLabeler.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o CMakeFiles/testCIPLabeler.dir/Node.cpp.o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -o testCIPLabeler ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 46%] Built target testCIPLabeler -make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ForceField/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 47%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceField_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o -MF CMakeFiles/rdForceField.dir/ForceField.cpp.o.d -o CMakeFiles/rdForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/Wrap/ForceField.cpp -[ 47%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Wrap/Conformer.cpp -[ 48%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp -[ 48%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so -[ 48%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DistGeom/DistViolationContrib.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2022.09.3 CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o CMakeFiles/Fingerprints.dir/MACCS.cpp.o CMakeFiles/Fingerprints.dir/MHFP.cpp.o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 48%] Built target Fingerprints -make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/DependInfo.cmake --color= +[ 45%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Depictor/EmbeddedFrag.cpp +[ 45%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o -MF CMakeFiles/rdchem.dir/RingInfo.cpp.o.d -o CMakeFiles/rdchem.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/RingInfo.cpp +[ 45%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/CoordGen/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdCoordGen.so CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 48%] Building CXX object Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDepictor_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp -[ 48%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 45%] Built target rdCoordGen +[ 46%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o -MF CMakeFiles/rdchem.dir/EditableMol.cpp.o.d -o CMakeFiles/rdchem.dir/EditableMol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/EditableMol.cpp +[ 46%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -MF CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o.d -o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DistGeom/TriangleSmooth.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4838,21 +4808,14 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/RingInfo.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 48%] Built target FilterCatalog -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 48%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFingerprintGenerator_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp +[ 46%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o +[ 46%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DistGeom/DistViolationContrib.cpp +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -MF CMakeFiles/rdchem.dir/MonomerInfo.cpp.o.d -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MonomerInfo.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4867,12 +4830,18 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/EditableMol.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MolFileStereochem.cpp +[ 46%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DistGeom/ChiralViolationContrib.cpp +[ 46%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -MF CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o.d -o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp +[ 46%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o -MF CMakeFiles/Depictor.dir/DepictUtils.cpp.o.d -o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/DepictUtils.cpp +[ 46%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o -MF CMakeFiles/rdchem.dir/MolBundle.cpp.o.d -o CMakeFiles/rdchem.dir/MolBundle.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MolBundle.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4887,10 +4856,26 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/ForceField/Wrap/ForceField.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MonomerInfo.cpp:13: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 46%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2022.09.3 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../lib/libRDKitForceField.so.1.2022.09.3 ../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 46%] Built target DistGeometry +make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ForceField/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 47%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceField_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o -MF CMakeFiles/rdForceField.dir/ForceField.cpp.o.d -o CMakeFiles/rdForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/Wrap/ForceField.cpp +[ 47%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o -MF CMakeFiles/rdchem.dir/StereoGroup.cpp.o.d -o CMakeFiles/rdchem.dir/StereoGroup.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/StereoGroup.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4904,21 +4889,33 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Conformer.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp:15: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 48%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DistGeom/ChiralViolationContrib.cpp -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-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' -[ 48%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMHFPFingerprint_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MolBundle.cpp:12: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4933,14 +4930,10 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/ForceField/Wrap/ForceField.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FileParsers/MolFileWriter.cpp -[ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4954,42 +4947,47 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:13: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/StereoGroup.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SDMolSupplier.cpp -[ 48%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolChemicalFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolChemicalFeatures.so CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o ../../../../lib/libRDKitMolChemicalFeatures.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 48%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2022.09.3 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../lib/libRDKitForceField.so.1.2022.09.3 ../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so +[ 47%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -MF CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SubstanceGroup.cpp +[ 47%] Linking CXX shared library ../../../lib/libRDKitDepictor.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/Depictor.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDepictor.so.1 -o ../../../lib/libRDKitDepictor.so.1.2022.09.3 CMakeFiles/Depictor.dir/RDDepictor.cpp.o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o CMakeFiles/Depictor.dir/DepictUtils.cpp.o ../../../lib/libRDKitMolAlign.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 48%] Built target DistGeometry -make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend +[ 47%] Built target Depictor +make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DistGeom /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build +make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 48%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceFieldHelpers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -MF CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o.d -o CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp +[ 47%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -MF CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o.d -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DistGeom/testDistGeom.cpp +[ 47%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Wrap/Chirality.cpp +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-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 48%] Built target rdMolChemicalFeatures -make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend +make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake --color= +[ 47%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeom_EXPORTS -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -MF CMakeFiles/DistGeom.dir/DistGeom.cpp.o.d -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap/DistGeom.cpp +make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build +make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 48%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DO3AAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -MF CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o.d -o CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp +[ 47%] Building CXX object Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDepictor_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5003,36 +5001,26 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SubstanceGroup.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FileParsers/SDWriter.cpp -[ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp -[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FileParsers/SmilesWriter.cpp -[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/TDTMolSupplier.cpp -[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FileParsers/TDTWriter.cpp -[ 49%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 47%] Linking CXX executable testDistGeom +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../lib/libRDKitForceField.so.1.2022.09.3 ../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 49%] Built target rdDepictor -make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend +[ 47%] Built target testDistGeom +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-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build +make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 49%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp +[ 47%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5047,31 +5035,10 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Chirality.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 49%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o -MF CMakeFiles/rdchem.dir/RingInfo.cpp.o.d -o CMakeFiles/rdchem.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/RingInfo.cpp -[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/TplFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/TplFileParser.cpp -[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/TplFileWriter.cpp -[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o -MF CMakeFiles/FileParsers.dir/PDBParser.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/PDBParser.cpp -[ 49%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 49%] Built target rdForceField -make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DistGeom /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 49%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -MF CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o.d -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DistGeom/testDistGeom.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5086,72 +5053,10 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/RingInfo.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -MF CMakeFiles/FileParsers.dir/PDBWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/PDBWriter.cpp -[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/PDBSupplier.cpp -[ 49%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2022.09.3 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2022.09.3 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 49%] Built target O3AAlign -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-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 49%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeom_EXPORTS -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -MF CMakeFiles/DistGeom.dir/DistGeom.cpp.o.d -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap/DistGeom.cpp -[ 49%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFingerprintGenerator.so CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 49%] Built target rdFingerprintGenerator -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-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CMLWriter.cpp.o -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CMLWriter.cpp.o -MF CMakeFiles/FileParsers.dir/CMLWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/CMLWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/CMLWriter.cpp -[ 50%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/XYZFileWriter.cpp -[ 50%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 50%] Built target rdForceFieldHelpers -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/XYZFileParser.cpp -[ 50%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Embedder.cpp -[ 51%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o -MF CMakeFiles/rdchem.dir/EditableMol.cpp.o.d -o CMakeFiles/rdchem.dir/EditableMol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/EditableMol.cpp -[ 51%] Linking CXX executable testDistGeom -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../lib/libRDKitForceField.so.1.2022.09.3 ../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 51%] Built target testDistGeom -[ 51%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -MF CMakeFiles/rdchem.dir/MonomerInfo.cpp.o.d -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MonomerInfo.cpp -[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MaeMolSupplier.cpp -[ 51%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMHFPFingerprint.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 51%] Built target rdMHFPFingerprint -[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -MF CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o.d -o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/ProximityBonds.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5170,10 +5075,25 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -MF CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o.d -o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SequenceParsers.cpp -[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FileParsers/SequenceWriters.cpp +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 47%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFingerprintGenerator_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp +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-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' +[ 47%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMHFPFingerprint_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp +[ 47%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5189,12 +5109,33 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 47%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FileParsers/SVGParser.cpp -[ 52%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 47%] Built target DistGeom +make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 47%] Built target rdForceField +[ 47%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o +make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceFieldHelpers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -MF CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o.d -o CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 47%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DO3AAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -MF CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o.d -o CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp +[ 48%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, @@ -5209,15 +5150,26 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/EditableMol.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:13: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o -MF CMakeFiles/FileParsers.dir/PNGParser.cpp.o.d -o CMakeFiles/FileParsers.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/PNGParser.cpp -[ 52%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -MF CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o.d -o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 48%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 48%] Built target rdDepictor +make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 48%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5231,24 +5183,13 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MonomerInfo.cpp:13: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 52%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 52%] Built target DistGeom -[ 52%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o -MF CMakeFiles/rdchem.dir/MolBundle.cpp.o.d -o CMakeFiles/rdchem.dir/MolBundle.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MolBundle.cpp -[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FileParsers/MultithreadedMolSupplier.cpp -[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp -[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5263,14 +5204,10 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp:31: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 53%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o -MF CMakeFiles/rdchem.dir/StereoGroup.cpp.o.d -o CMakeFiles/rdchem.dir/StereoGroup.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/StereoGroup.cpp -[ 53%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -MF CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SubstanceGroup.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5284,17 +5221,11 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp:15: + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp:31: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 53%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Wrap/Chirality.cpp -[ 53%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5302,19 +5233,21 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MolBundle.cpp:12: + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 48%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp +[ 48%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdchem.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdchem.so CMakeFiles/rdchem.dir/rdchem.cpp.o CMakeFiles/rdchem.dir/Table.cpp.o CMakeFiles/rdchem.dir/Atom.cpp.o CMakeFiles/rdchem.dir/Bond.cpp.o CMakeFiles/rdchem.dir/Mol.cpp.o CMakeFiles/rdchem.dir/Conformer.cpp.o CMakeFiles/rdchem.dir/RingInfo.cpp.o CMakeFiles/rdchem.dir/EditableMol.cpp.o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o CMakeFiles/rdchem.dir/MolBundle.cpp.o CMakeFiles/rdchem.dir/StereoGroup.cpp.o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o CMakeFiles/rdchem.dir/Chirality.cpp.o ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5328,13 +5261,58 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SubstanceGroup.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 48%] Built target rdchem +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-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FileParsers/CDXMLParser.cpp +[ 48%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 48%] Built target rdForceFieldHelpers +make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 48%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp +[ 48%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2022.09.3 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2022.09.3 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 48%] Built target O3AAlign +[ 48%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Embedder.cpp +[ 48%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp +[ 48%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFingerprintGenerator.so CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 48%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMHFPFingerprint.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 48%] Built target rdFingerprintGenerator +[ 49%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 49%] Built target rdMHFPFingerprint +[ 49%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5342,19 +5320,14 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/StereoGroup.cpp:12: + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.h:24, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Embedder.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5369,7 +5342,7 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Chirality.cpp:10: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -5380,680 +5353,860 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.h:24, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Embedder.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp:10: + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 53%] Linking CXX shared library ../../../lib/libRDKitFileParsers.so +[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FileParsers/Mol2FileParser.cpp +[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FileParsers/MolFileParser.cpp +[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FileParsers/MolSGroupParsing.cpp +[ 50%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolChemicalFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolChemicalFeatures.so CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o ../../../../lib/libRDKitMolChemicalFeatures.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 50%] Built target rdMolChemicalFeatures +[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FileParsers/MolSGroupWriting.cpp +[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MolFileStereochem.cpp +[ 51%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 51%] Built target DistGeomHelpers +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FileParsers/MolFileWriter.cpp +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SDMolSupplier.cpp +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FileParsers/SDWriter.cpp +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FileParsers/SmilesWriter.cpp +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/TDTMolSupplier.cpp +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FileParsers/TDTWriter.cpp +[ 52%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 52%] Built target rdfiltercatalog +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/TplFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/TplFileParser.cpp +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/TplFileWriter.cpp +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o -MF CMakeFiles/FileParsers.dir/PDBParser.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/PDBParser.cpp +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -MF CMakeFiles/FileParsers.dir/PDBWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/PDBWriter.cpp +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/PDBSupplier.cpp +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CMLWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CMLWriter.cpp.o -MF CMakeFiles/FileParsers.dir/CMLWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/CMLWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/CMLWriter.cpp +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/XYZFileWriter.cpp +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/XYZFileParser.cpp +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MaeMolSupplier.cpp +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -MF CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o.d -o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/ProximityBonds.cpp +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -MF CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o.d -o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SequenceParsers.cpp +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FileParsers/SequenceWriters.cpp +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FileParsers/SVGParser.cpp +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o -MF CMakeFiles/FileParsers.dir/PNGParser.cpp.o.d -o CMakeFiles/FileParsers.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/PNGParser.cpp +[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FileParsers/MultithreadedMolSupplier.cpp +[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp +[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp +[ 54%] Linking CXX shared library ../../../lib/libRDKitFileParsers.so cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/FileParsers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFileParsers.so.1 -o ../../../lib/libRDKitFileParsers.so.1.2022.09.3 CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDWriter.cpp.o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o CMakeFiles/FileParsers.dir/PDBParser.cpp.o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o CMakeFiles/FileParsers.dir/CMLWriter.cpp.o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o CMakeFiles/FileParsers.dir/SVGParser.cpp.o CMakeFiles/FileParsers.dir/PNGParser.cpp.o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1 ../../../lib/libRDKitFileParsers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 53%] Built target FileParsers +[ 54%] Built target FileParsers make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/depend make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend +make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend -make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/External/CoordGen /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/UFF /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/UFF/CMakeFiles/testUFFForceField.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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/External/CoordGen /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake --color= -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake --color= -make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/MMFF /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/build -make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/build -make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 55%] Building CXX object External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o +[ 55%] Building CXX object Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/CoordGen && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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 External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o -MF CMakeFiles/testCoordGen.dir/test.cpp.o.d -o CMakeFiles/testCoordGen.dir/test.cpp.o -c /build/reproducible-path/rdkit-202209.3/External/CoordGen/test.cpp +[ 55%] Building CXX object Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/MMFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -MF CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o.d -o CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/testMMFFForceField.cpp +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/UFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/ForceField/UFF/testUFFForceField.cpp +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/graphmolTest1.dir/test1.cpp.o -MF CMakeFiles/graphmolTest1.dir/test1.cpp.o.d -o CMakeFiles/graphmolTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/test1.cpp +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -MF CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o.d -o CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testChirality.cpp +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/graphmoltestPickler.dir/testPickler.cpp.o -MF CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o.d -o CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPickler.cpp +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -MF CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o.d -o CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/molopstest.cpp +[ 55%] Linking CXX executable testCoordGen +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/CoordGen && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoordGen.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCoordGen.dir/test.cpp.o -o testCoordGen /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 55%] Built target testCoordGen +make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -MF CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o.d -o CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPicklerGlobalSettings.cpp +[ 55%] Linking CXX executable testUFFForceField +cd /build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -o testUFFForceField ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 55%] Built target testUFFForceField +make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/hanoiTest.dir/hanoitest.cpp.o -MF CMakeFiles/hanoiTest.dir/hanoitest.cpp.o.d -o CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/hanoitest.cpp +[ 56%] Linking CXX executable graphmolTest1 +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolTest1.dir/test1.cpp.o -o graphmolTest1 ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../lib/libRDKitForceField.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 56%] Built target graphmolTest1 +make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 56%] Building CXX object Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -MF CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o.d -o CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/resMolSupplierTest.cpp +[ 56%] Linking CXX executable testMMFFForceField +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -o testMMFFForceField ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 56%] Built target testMMFFForceField +make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 53%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -MF CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o.d -o CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testChirality.cpp -[ 53%] Building CXX object Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/UFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/ForceField/UFF/testUFFForceField.cpp -[ 54%] Building CXX object External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o -[ 54%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -[ 54%] Building CXX object Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -[ 54%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -[ 54%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -MF CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o.d -o CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/molopstest.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/CoordGen && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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 External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o -MF CMakeFiles/testCoordGen.dir/test.cpp.o.d -o CMakeFiles/testCoordGen.dir/test.cpp.o -c /build/reproducible-path/rdkit-202209.3/External/CoordGen/test.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -MF CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o.d -o CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/resMolSupplierTest.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -MF CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o.d -o CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPicklerGlobalSettings.cpp -[ 54%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/graphmolTest1.dir/test1.cpp.o -MF CMakeFiles/graphmolTest1.dir/test1.cpp.o.d -o CMakeFiles/graphmolTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/test1.cpp -[ 54%] Building CXX object Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -[ 54%] Building CXX object Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/hanoiTest.dir/hanoitest.cpp.o -MF CMakeFiles/hanoiTest.dir/hanoitest.cpp.o.d -o CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/hanoitest.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/graphmoltestPickler.dir/testPickler.cpp.o -MF CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o.d -o CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPickler.cpp +[ 56%] Building CXX object Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/molBundleTest.dir/testMolBundle.cpp.o -MF CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o.d -o CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testMolBundle.cpp +[ 56%] Linking CXX executable graphmoltestPicklerGlobalSetting +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -o graphmoltestPicklerGlobalSetting ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 56%] Built target graphmoltestPicklerGlobalSetting make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 54%] Building CXX object Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o +[ 56%] Building CXX object Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/testSGroup.dir/testSGroup.cpp.o -MF CMakeFiles/testSGroup.dir/testSGroup.cpp.o.d -o CMakeFiles/testSGroup.dir/testSGroup.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testSGroup.cpp +[ 56%] Linking CXX executable hanoiTest +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/hanoiTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 56%] Built target hanoiTest make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 54%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o +[ 56%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/graphmolTestsCatch.dir/catch_graphmol.cpp.o -MF CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o.d -o CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/catch_graphmol.cpp -[ 55%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so +[ 56%] Linking CXX executable graphmoltestPickler +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 55%] Built target DistGeomHelpers +[ 56%] Built target graphmoltestPickler make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o +[ 56%] Building CXX object Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -MF CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o.d -o CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/catch_sgroups.cpp +[ 57%] Linking CXX executable resMolSupplierTest +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -o resMolSupplierTest ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 58%] Linking CXX executable graphmoltestChirality +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 58%] Built target resMolSupplierTest make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o +[ 58%] Building CXX object Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -MF CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o.d -o CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/catch_adjustquery.cpp -[ 55%] Linking CXX executable molBundleTest -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molBundleTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -o molBundleTest ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 55%] Built target molBundleTest +[ 58%] Built target graphmoltestChirality make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 56%] Building CXX object Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o +[ 59%] Building CXX object Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/chiralityTestsCatch.dir/catch_chirality.cpp.o -MF CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o.d -o CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/catch_chirality.cpp -[ 57%] Linking CXX executable resMolSupplierTest -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -o resMolSupplierTest ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 59%] Linking CXX executable molBundleTest +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molBundleTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -o molBundleTest ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 57%] Built target resMolSupplierTest +[ 59%] Built target molBundleTest make -f Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/canonTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/canonTestsCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 57%] Building CXX object Code/GraphMol/CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o +[ 59%] Building CXX object Code/GraphMol/CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/canonTestsCatch.dir/catch_canon.cpp.o -MF CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o.d -o CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/catch_canon.cpp -[ 57%] Linking CXX executable graphmoltestPicklerGlobalSetting -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -o graphmoltestPicklerGlobalSetting ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 59%] Linking CXX executable canonTestsCatch +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/canonTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -o canonTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 57%] Built target graphmoltestPicklerGlobalSetting +[ 59%] Built target canonTestsCatch make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 58%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o +[ 60%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o -MF CMakeFiles/testDepictor.dir/testDepictor.cpp.o.d -o CMakeFiles/testDepictor.dir/testDepictor.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/testDepictor.cpp -[ 58%] Linking CXX executable testCoordGen -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/CoordGen && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoordGen.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCoordGen.dir/test.cpp.o -o testCoordGen /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libz.so +[ 60%] Linking CXX executable graphmolSGroupCatch +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolSGroupCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -o graphmolSGroupCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 58%] Built target testCoordGen +[ 60%] Built target graphmolSGroupCatch 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/build.make Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 58%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/catch_tests.cpp.o +[ 60%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -MF CMakeFiles/depictorCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/catch_tests.cpp -[ 58%] Linking CXX executable hanoiTest -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/hanoiTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so -[ 58%] Linking CXX executable testUFFForceField -cd /build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -o testUFFForceField ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 60%] Linking CXX executable graphmolAdjustQueryCatch +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolAdjustQueryCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -o graphmolAdjustQueryCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 58%] Built target hanoiTest +[ 60%] Built target graphmolAdjustQueryCatch 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 58%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/test.cpp.o +[ 60%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/test.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/test.cpp.o -MF CMakeFiles/smiTest1.dir/test.cpp.o.d -o CMakeFiles/smiTest1.dir/test.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/test.cpp +[ 60%] Linking CXX executable testSGroup +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSGroup.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSGroup.dir/testSGroup.cpp.o -o testSGroup ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 58%] Built target testUFFForceField +[ 60%] Built target testSGroup make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 58%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o +[ 60%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -MF CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o.d -o CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/cxsmiles_test.cpp -[ 58%] Linking CXX executable graphmolSGroupCatch -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolSGroupCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -o graphmolSGroupCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 60%] Linking CXX executable depictorCatch +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/depictorCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -o depictorCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 58%] Built target graphmolSGroupCatch +[ 60%] Built target depictorCatch 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 58%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o +[ 60%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/catch_tests.cpp -[ 58%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdchem.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdchem.so CMakeFiles/rdchem.dir/rdchem.cpp.o CMakeFiles/rdchem.dir/Table.cpp.o CMakeFiles/rdchem.dir/Atom.cpp.o CMakeFiles/rdchem.dir/Bond.cpp.o CMakeFiles/rdchem.dir/Mol.cpp.o CMakeFiles/rdchem.dir/Conformer.cpp.o CMakeFiles/rdchem.dir/RingInfo.cpp.o CMakeFiles/rdchem.dir/EditableMol.cpp.o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o CMakeFiles/rdchem.dir/MolBundle.cpp.o CMakeFiles/rdchem.dir/StereoGroup.cpp.o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o CMakeFiles/rdchem.dir/Chirality.cpp.o ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 60%] Linking CXX executable testDepictor +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDepictor.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDepictor.dir/testDepictor.cpp.o -o testDepictor ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 58%] Built target rdchem +[ 60%] Built target testDepictor 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 58%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o +[ 60%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -MF CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o.d -o CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/nontetrahedral_tests.cpp -[ 58%] Linking CXX executable graphmolAdjustQueryCatch -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolAdjustQueryCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -o graphmolAdjustQueryCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so -[ 59%] Linking CXX executable graphmolTest1 -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolTest1.dir/test1.cpp.o -o graphmolTest1 ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../lib/libRDKitForceField.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 60%] Linking CXX executable cxsmilesTest +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/cxsmilesTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -o cxsmilesTest ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 59%] Built target graphmolAdjustQueryCatch +[ 60%] Built target cxsmilesTest 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 59%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o +[ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/fileParsersTest1.dir/test1.cpp.o -MF CMakeFiles/fileParsersTest1.dir/test1.cpp.o.d -o CMakeFiles/fileParsersTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/test1.cpp +[ 60%] Linking CXX executable graphmolTestsCatch +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -o graphmolTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 59%] Built target graphmolTest1 +[ 60%] Built target graphmolTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o +[ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -MF CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o.d -o CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/testMolSupplier.cpp -[ 60%] Linking CXX executable testSGroup -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSGroup.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSGroup.dir/testSGroup.cpp.o -o testSGroup ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 61%] Linking CXX executable nontetrahedralCatch +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/nontetrahedralCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -o nontetrahedralCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 60%] Built target testSGroup +[ 61%] Built target nontetrahedralCatch 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o +[ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -MF CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o.d -o CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/testGeneralFileReader.cpp -[ 60%] Linking CXX executable depictorCatch -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/depictorCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -o depictorCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libz.so +[ 61%] Linking CXX executable chiralityTestsCatch +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/chiralityTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -o chiralityTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 60%] Built target depictorCatch +[ 61%] Built target chiralityTestsCatch 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o +[ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -MF CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o.d -o CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/testMultithreadedMolSupplier.cpp -[ 61%] Linking CXX executable canonTestsCatch -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/canonTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -o canonTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 62%] Linking CXX executable graphmolMolOpsTest +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 61%] Built target canonTestsCatch +[ 62%] Built target graphmolMolOpsTest 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o +[ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -MF CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o.d -o CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/testMolWriter.cpp -[ 61%] Linking CXX executable cxsmilesTest -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/cxsmilesTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -o cxsmilesTest ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 62%] Linking CXX executable testGeneralFileReader +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -o testGeneralFileReader ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitRDStreams.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 61%] Built target cxsmilesTest +[ 62%] Built target testGeneralFileReader make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o +[ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o -MF CMakeFiles/testTplParser.dir/testTpls.cpp.o.d -o CMakeFiles/testTplParser.dir/testTpls.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/testTpls.cpp -[ 61%] Linking CXX executable testDepictor -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDepictor.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDepictor.dir/testDepictor.cpp.o -o testDepictor ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libz.so +[ 62%] Linking CXX executable testMolSupplier +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolSupplier.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitRDStreams.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 61%] Built target testDepictor +[ 62%] Built target testMolSupplier 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o +[ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -MF CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o.d -o CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/testMol2ToMol.cpp -[ 61%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 62%] Linking CXX executable testMultithreadedMolSupplier +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitRDStreams.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 61%] Built target rdfiltercatalog +[ 62%] Built target testMultithreadedMolSupplier make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o +[ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/GraphMol/FileParsers/testSequence.cpp -[ 61%] Linking CXX executable nontetrahedralCatch -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/nontetrahedralCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -o nontetrahedralCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 62%] Linking CXX executable testTplParser +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 61%] Built target nontetrahedralCatch +[ 62%] Built target testTplParser 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o +[ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -MF CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o.d -o CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp -[ 61%] Linking CXX executable graphmoltestPickler -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 63%] Linking CXX executable smiTest1 +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTest1.dir/test.cpp.o -o smiTest1 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 61%] Built target graphmoltestPickler +[ 63%] Built target smiTest1 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o +[ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -MF CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o.d -o CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/file_parsers_catch.cpp -[ 61%] Linking CXX executable testMultithreadedMolSupplier -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitRDStreams.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -[ 61%] Linking CXX executable testGeneralFileReader -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -o testGeneralFileReader ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitRDStreams.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so +[ 63%] Linking CXX executable smiTestCatch +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -o smiTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 61%] Built target testMultithreadedMolSupplier +[ 63%] Built target smiTestCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o +[ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -MF CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o.d -o CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/testPropertyLists.cpp +[ 63%] Linking CXX executable testSequence +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSequence.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSequence.dir/testSequence.cpp.o -o testSequence ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 61%] Built target testGeneralFileReader +[ 63%] Built target testSequence make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o +[ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -MF CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o.d -o CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/XYZFileParserCatchTest.cpp -[ 62%] Linking CXX executable graphmoltestChirality -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 63%] Linking CXX executable testMol2ToMol +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 62%] Built target graphmoltestChirality +[ 63%] Linking CXX executable testExtendedStereoParsing +[ 63%] Built target testMol2ToMol +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/DependInfo.cmake --color= +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -o testExtendedStereoParsing ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o +[ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/GraphMol/FileParsers/cdxml_parser_catch.cpp -[ 62%] Linking CXX executable testTplParser -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 62%] Built target testTplParser +[ 63%] Built target testExtendedStereoParsing make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 62%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o +[ 63%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o -MF CMakeFiles/testSubstructMatch.dir/test1.cpp.o.d -o CMakeFiles/testSubstructMatch.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/test1.cpp -[ 62%] Linking CXX executable testSequence -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSequence.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSequence.dir/testSequence.cpp.o -o testSequence ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 63%] Linking CXX executable testMolWriter +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 62%] Built target testSequence +[ 63%] Built target testMolWriter 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 63%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o +[ 64%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/catch_tests.cpp -[ 63%] Linking CXX executable testExtendedStereoParsing -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -o testExtendedStereoParsing ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 64%] Linking CXX executable XYZFileParserCatchTest +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/XYZFileParserCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -o XYZFileParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 63%] Built target testExtendedStereoParsing +[ 64%] Built target XYZFileParserCatchTest 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 63%] Building CXX object Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o +[ 64%] Building CXX object Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/GenericGroups/CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -MF CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o.d -o CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/GenericGroups/generic_tests.cpp -[ 63%] Linking CXX executable testMol2ToMol -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 65%] Linking CXX executable fileParsersTest1 +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 63%] Built target testMol2ToMol +[ 65%] Built target fileParsersTest1 make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 63%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Crippen.cpp.o +[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Crippen.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Crippen.cpp.o -MF CMakeFiles/Descriptors.dir/Crippen.cpp.o.d -o CMakeFiles/Descriptors.dir/Crippen.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Crippen.cpp -[ 63%] Linking CXX executable graphmolTestsCatch -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -o graphmolTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 65%] Linking CXX executable substructTestCatch +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -o substructTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 63%] Built target graphmolTestsCatch +[ 65%] Built target substructTestCatch make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 63%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o +[ 65%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -MF CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o.d -o CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms/testChemTransforms.cpp -[ 63%] Linking CXX executable XYZFileParserCatchTest -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/XYZFileParserCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -o XYZFileParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 65%] Linking CXX executable cdxmlParserCatchTest +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/cdxmlParserCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -o cdxmlParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 63%] Built target XYZFileParserCatchTest +[ 65%] Built target cdxmlParserCatchTest make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 63%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o +[ 65%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms/catch_tests.cpp -[ 63%] Linking CXX executable testMolWriter -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 65%] Linking CXX executable testPropertyLists +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPropertyLists.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -o testPropertyLists ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 63%] Built target testMolWriter +[ 65%] Built target testPropertyLists make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 63%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o +[ 65%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -MF CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o.d -o CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp -[ 63%] Linking CXX executable substructTestCatch -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -o substructTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so -[ 63%] Linking CXX executable cdxmlParserCatchTest -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/cdxmlParserCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -o cdxmlParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 65%] Linking CXX executable testSubstructMatch +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSubstructMatch.dir/test1.cpp.o -o testSubstructMatch ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 63%] Built target substructTestCatch +[ 65%] Built target testSubstructMatch make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 64%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o +[ 66%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o -MF CMakeFiles/testFragCatalog.dir/test1.cpp.o.d -o CMakeFiles/testFragCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/test1.cpp +[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -MF CMakeFiles/Descriptors.dir/BCUT.cpp.o.d -o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/BCUT.cpp +[ 66%] Linking CXX executable testGenericGroups +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGenericGroups.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -o testGenericGroups ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 64%] Built target cdxmlParserCatchTest +[ 66%] Built target testGenericGroups make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend -[ 64%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake --color= -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -MF CMakeFiles/Descriptors.dir/BCUT.cpp.o.d -o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/BCUT.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 64%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o +[ 66%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.cpp -[ 64%] Linking CXX executable testGenericGroups -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGenericGroups.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -o testGenericGroups ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.h:15, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.cpp:11: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 66%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp +[ 66%] Linking CXX executable filterCatalogTest +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -o filterCatalogTest ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 64%] Built target testGenericGroups +[ 66%] Built target filterCatalogTest make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 64%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o +[ 66%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/GraphMol/Fingerprints/test1.cpp -[ 64%] Linking CXX executable testPropertyLists -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPropertyLists.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -o testPropertyLists ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 66%] Linking CXX executable chemTransformsTestCatch +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemTransformsTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -o chemTransformsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 64%] Built target testPropertyLists +[ 66%] Built target chemTransformsTestCatch 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 64%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o +[ 66%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -MF CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o.d -o CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/testMHFPFingerprint.cpp -[ 64%] Linking CXX executable testMolSupplier -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolSupplier.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitRDStreams.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so +[ 66%] Linking CXX executable testFragCatalog +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFragCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFragCatalog.dir/test1.cpp.o -o testFragCatalog ../../../lib/libRDKitFragCatalog.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp:12: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 64%] Built target testMolSupplier +[ 66%] Built target testFragCatalog make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 64%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o +[ 66%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp -[ 64%] Linking CXX executable smiTestCatch -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -o smiTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 66%] Linking CXX executable fileParsersCatchTest +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -o fileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 66%] Linking CXX executable testChemTransforms +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -o testChemTransforms ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 64%] Built target smiTestCatch +[ 66%] Built target fileParsersCatchTest 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 64%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o +[ 66%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/GraphMol/Fingerprints/catch_tests.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.h:15, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.cpp:11: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 64%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp -[ 64%] Linking CXX executable testSubstructMatch -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSubstructMatch.dir/test1.cpp.o -o testSubstructMatch ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 64%] Built target testSubstructMatch +[ 66%] Built target testChemTransforms make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 64%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o +[ 66%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o -MF CMakeFiles/testMolTransforms.dir/test1.cpp.o.d -o CMakeFiles/testMolTransforms.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp -[ 64%] Linking CXX executable chiralityTestsCatch -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/chiralityTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -o chiralityTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so -[ 64%] Linking CXX executable testMHFPFingerprint +[ 66%] Linking CXX executable testMHFPFingerprint cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMHFPFingerprint.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -o testMHFPFingerprint ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 64%] Built target testMHFPFingerprint +[ 66%] Built target testMHFPFingerprint make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 64%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o +[ 66%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp +[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MolDescriptors.cpp +[ 66%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp +[ 66%] Linking CXX executable testMolTransforms +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolTransforms.dir/test1.cpp.o -o testMolTransforms ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp:10: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 64%] Built target chiralityTestsCatch +[ 66%] Built target testMolTransforms make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake --color= -[ 64%] Linking CXX executable chemTransformsTestCatch -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemTransformsTestCatch.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -o chemTransformsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 64%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o +[ 66%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp +[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o -MF CMakeFiles/Descriptors.dir/MolSurf.cpp.o.d -o CMakeFiles/Descriptors.dir/MolSurf.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MolSurf.cpp +[ 67%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp +[ 67%] Linking CXX executable fpTestCatch +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -o fpTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 67%] Linking CXX executable testMMFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -o testMMFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 64%] Built target chemTransformsTestCatch +[ 67%] Built target fpTestCatch make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 64%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o +[ 67%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp -[ 65%] Linking CXX executable smiTest1 -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTest1.dir/test.cpp.o -o smiTest1 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so -[ 65%] Linking CXX executable filterCatalogTest -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -o filterCatalogTest ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 65%] Built target smiTest1 +[ 67%] Built target testMMFFForceFieldHelpers 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 65%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o +[ 67%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp +[ 67%] Linking CXX executable testFingerprintGenerators +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprintGenerators.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 65%] Built target filterCatalogTest +[ 67%] Built target testFingerprintGenerators 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 65%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o +[ 67%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -MF CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o.d -o CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp +[ 68%] Linking CXX executable testMMFFForceFieldHelpersMultiThread +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -o testMMFFForceFieldHelpersMultiThread ../../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 68%] Built target testMMFFForceFieldHelpersMultiThread +make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 68%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -MF CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/catch_tests.cpp +[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Descriptors/Lipinski.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6068,92 +6221,40 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 65%] Linking CXX executable testFragCatalog -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFragCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFragCatalog.dir/test1.cpp.o -o testFragCatalog ../../../lib/libRDKitFragCatalog.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 65%] Built target testFragCatalog -make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 65%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -MF CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/catch_tests.cpp -[ 65%] Linking CXX executable testChemTransforms -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -o testChemTransforms ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 68%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp +[ 68%] Linking CXX executable testCrystalForceField +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -o testCrystalForceField ../../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 65%] Built target testChemTransforms +[ 68%] Built target testCrystalForceField make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 65%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o +[ 68%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/c++ -DBOOST_PYTHON_MAX_ARITY=32 -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDistGeom_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -MF CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o.d -o CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp -[ 66%] Linking CXX executable testMMFFForceFieldHelpersMultiThread -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -o testMMFFForceFieldHelpersMultiThread ../../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so -[ 66%] Linking CXX executable testMolTransforms -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolTransforms.dir/test1.cpp.o -o testMolTransforms ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 68%] Linking CXX executable testFingerprints +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprints.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFingerprints.dir/test1.cpp.o -o testFingerprints ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 66%] Built target testMolTransforms +[ 68%] Built target testFingerprints make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/depend -[ 66%] Built target testMMFFForceFieldHelpersMultiThread -make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 66%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o -[ 66%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o -MF CMakeFiles/testFeatures.dir/testFeatures.cpp.o.d -o CMakeFiles/testFeatures.dir/testFeatures.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp +[ 68%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/catch_tests.cpp -[ 66%] Linking CXX executable testCrystalForceField -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -o testCrystalForceField ../../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 66%] Built target testCrystalForceField -make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 66%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -MF CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o.d -o CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/testShapeHelpers.cpp -[ 66%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp -[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MolDescriptors.cpp -[ 66%] Linking CXX executable fpTestCatch -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -o fpTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 66%] Built target fpTestCatch -make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 66%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o -MF CMakeFiles/testMolCatalog.dir/test1.cpp.o.d -o CMakeFiles/testMolCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/test1.cpp +[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6168,10 +6269,23 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:10: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 68%] Linking CXX executable distGeomHelpersCatch +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/distGeomHelpersCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -o distGeomHelpersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 68%] Built target distGeomHelpersCatch +make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 68%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o -MF CMakeFiles/testFeatures.dir/testFeatures.cpp.o.d -o CMakeFiles/testFeatures.dir/testFeatures.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6186,133 +6300,170 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp:10: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 66%] Linking CXX executable graphmolMolOpsTest -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so -[ 66%] Linking CXX executable testFingerprintGenerators -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprintGenerators.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 68%] Linking CXX executable testUFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 68%] Built target testUFFForceFieldHelpers +make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 68%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -MF CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o.d -o CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/testShapeHelpers.cpp +[ 68%] Linking CXX executable molAlignCatchTest +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/molAlignCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -o molAlignCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 68%] Built target molAlignCatchTest +make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 68%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o -MF CMakeFiles/testMolCatalog.dir/test1.cpp.o.d -o CMakeFiles/testMolCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/test1.cpp +[ 68%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfragcatalog.so CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o ../../../../lib/libRDKitFragCatalog.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 66%] Built target testFingerprintGenerators +[ 68%] Built target rdfragcatalog make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 66%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o +[ 68%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o -MF CMakeFiles/FMCS.dir/FMCS.cpp.o.d -o CMakeFiles/FMCS.dir/FMCS.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/FMCS.cpp -[ 66%] Built target graphmolMolOpsTest +[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o -MF CMakeFiles/Descriptors.dir/MQN.cpp.o.d -o CMakeFiles/Descriptors.dir/MQN.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MQN.cpp +In file included from /usr/include/boost/bind.hpp:30, + from /usr/include/boost/property_tree/json_parser/detail/parser.hpp:7, + from /usr/include/boost/property_tree/json_parser/detail/read.hpp:13, + from /usr/include/boost/property_tree/json_parser.hpp:16, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/FMCS.cpp:16: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 68%] Linking CXX executable testShapeHelpers +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testShapeHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -o testShapeHelpers ../../../lib/libRDKitShapeHelpers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 68%] Built target testShapeHelpers make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 66%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o +[ 68%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMMPA_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MMPA_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o -MF CMakeFiles/MMPA.dir/MMPA.cpp.o.d -o CMakeFiles/MMPA.dir/MMPA.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/MMPA.cpp -[ 66%] Linking CXX executable testUFFForceFieldHelpers -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so -[ 66%] Linking CXX executable testMMFFForceFieldHelpers -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -o testMMFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 68%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDistGeom.so CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o ../../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 66%] Built target testUFFForceFieldHelpers +[ 68%] Built target rdDistGeom make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/DependInfo.cmake --color= -[ 67%] Linking CXX executable fileParsersTest1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so -[ 67%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o +[ 68%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -MF CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o.d -o CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/trajectoryTest.cpp +[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o -MF CMakeFiles/Descriptors.dir/Property.cpp.o.d -o CMakeFiles/Descriptors.dir/Property.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Property.cpp +[ 68%] Linking CXX executable testMolCatalog +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog ../../../lib/libRDKitMolCatalog.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 67%] Built target testMMFFForceFieldHelpers +[ 68%] Built target testMolCatalog make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 67%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o +[ 68%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -MF CMakeFiles/molInterchangeTest1.dir/test1.cpp.o.d -o CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange/test1.cpp +[ 68%] Linking CXX executable testFeatures +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFeatures.dir/testFeatures.cpp.o -o testFeatures ../../../lib/libRDKitMolChemicalFeatures.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 67%] Built target fileParsersTest1 +[ 68%] Built target testFeatures make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 67%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o +[ 68%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/rapidjson -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/GraphMol/MolInterchange/molinterchange_catch.cpp -[ 67%] Linking CXX executable distGeomHelpersCatch -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/distGeomHelpersCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -o distGeomHelpersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so -[ 67%] Linking CXX executable fileParsersCatchTest -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -o fileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 69%] Linking CXX executable testDistGeomHelpers +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeomHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -o testDistGeomHelpers ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 67%] Built target distGeomHelpersCatch +[ 69%] Built target testDistGeomHelpers make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 67%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o +[ 69%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -MF CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o.d -o CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdmolfiles.cpp +[ 69%] Linking CXX shared library ../../../lib/libRDKitMMPA.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMMPA.so.1 -o ../../../lib/libRDKitMMPA.so.1.2022.09.3 CMakeFiles/MMPA.dir/MMPA.cpp.o ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libz.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2022.09.3 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 67%] Built target fileParsersCatchTest +[ 69%] Built target MMPA make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 67%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o +[ 69%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -MF CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o.d -o CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/catch_tests.cpp -[ 67%] Linking CXX executable testShapeHelpers -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testShapeHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -o testShapeHelpers ../../../lib/libRDKitShapeHelpers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so +[ 70%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o -MF CMakeFiles/FMCS.dir/Seed.cpp.o.d -o CMakeFiles/FMCS.dir/Seed.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Seed.cpp +[ 70%] Linking CXX executable molInterchangeCatchTest +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -o molInterchangeCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolInterchange.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 67%] Built target testShapeHelpers -make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend +[ 70%] Built target molInterchangeCatchTest +make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/MMFF /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build +make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 67%] Building CXX object Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/MMFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -MF CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o.d -o CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/testMMFFForceField.cpp -[ 67%] Linking CXX executable molAlignCatchTest -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/molAlignCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -o molAlignCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so -[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o -MF CMakeFiles/Descriptors.dir/MolSurf.cpp.o.d -o CMakeFiles/Descriptors.dir/MolSurf.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MolSurf.cpp -In file included from /usr/include/boost/bind.hpp:30, - from /usr/include/boost/property_tree/json_parser/detail/parser.hpp:7, - from /usr/include/boost/property_tree/json_parser/detail/read.hpp:13, - from /usr/include/boost/property_tree/json_parser.hpp:16, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/FMCS.cpp:16: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ +[ 70%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -MF CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o.d -o CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/MMPA_UnitTest.cpp +[ 71%] Linking CXX executable trajectoryTest +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -o trajectoryTest ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 68%] Built target molAlignCatchTest -[ 68%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp -[ 68%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp +[ 71%] Built target trajectoryTest +make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 71%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMMPA_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -MF CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o.d -o CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp +[ 71%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -MF CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o.d -o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/AUTOCORR2D.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6331,9 +6482,6 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 68%] Linking CXX executable testFeatures -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFeatures.dir/testFeatures.cpp.o -o testFeatures ../../../lib/libRDKitMolChemicalFeatures.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6347,211 +6495,67 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp:11: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 68%] Built target testFeatures -[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Descriptors/Lipinski.cpp -[ 68%] Linking CXX executable molInterchangeCatchTest -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -o molInterchangeCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolInterchange.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 68%] Built target molInterchangeCatchTest -[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp -[ 68%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDistGeom.so CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o ../../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 68%] Built target rdDistGeom -[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o -MF CMakeFiles/Descriptors.dir/MQN.cpp.o.d -o CMakeFiles/Descriptors.dir/MQN.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MQN.cpp -[ 68%] Linking CXX executable testMolCatalog -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog ../../../lib/libRDKitMolCatalog.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 68%] Built target testMolCatalog -[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o -MF CMakeFiles/Descriptors.dir/Property.cpp.o.d -o CMakeFiles/Descriptors.dir/Property.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Property.cpp -[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -MF CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o.d -o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/AUTOCORR2D.cpp -[ 69%] Linking CXX executable trajectoryTest -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -o trajectoryTest ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 69%] Built target trajectoryTest -[ 69%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 69%] Linking CXX shared library ../../../lib/libRDKitMMPA.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMMPA.so.1 -o ../../../lib/libRDKitMMPA.so.1.2022.09.3 CMakeFiles/MMPA.dir/MMPA.cpp.o ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libz.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2022.09.3 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 69%] Built target MMPA -make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 69%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -MF CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o.d -o CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/MMPA_UnitTest.cpp -[ 69%] Linking CXX executable testFingerprints -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprints.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFingerprints.dir/test1.cpp.o -o testFingerprints ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 69%] Built target testFingerprints -make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 69%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMMPA_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -MF CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o.d -o CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp -[ 69%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Data3Ddescriptors.cpp -[ 69%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MolData3Ddescriptors.cpp -[ 70%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o -MF CMakeFiles/FMCS.dir/Seed.cpp.o.d -o CMakeFiles/FMCS.dir/Seed.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Seed.cpp -[ 71%] Linking CXX executable testDistGeomHelpers -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeomHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -o testDistGeomHelpers ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 71%] Built target testDistGeomHelpers -[ 71%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -MF CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o.d -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ [ 71%] Linking CXX executable molInterchangeTest1 cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -o molInterchangeTest1 ../../../lib/libRDKitMolInterchange.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 71%] Built target molInterchangeTest1 -[ 71%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -MF CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o.d -o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/SubstructMatchCustom.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp:13: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ +[ 71%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Data3Ddescriptors.cpp +[ 71%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MolData3Ddescriptors.cpp +[ 71%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -MF CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o.d -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp [ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -MF CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o.d -o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/USRDescriptor.cpp -[ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfragcatalog.so CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o ../../../../lib/libRDKitFragCatalog.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 72%] Linking CXX executable testMMPA +cd /build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -o testMMPA ../../../lib/libRDKitMMPA.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 72%] Built target testMMPA [ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Descriptors/AtomFeat.cpp +[ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMMPA.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o ../../../../lib/libRDKitMMPA.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 72%] Built target rdfragcatalog +[ 72%] Built target rdMMPA [ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o -MF CMakeFiles/Descriptors.dir/EEM.cpp.o.d -o CMakeFiles/Descriptors.dir/EEM.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/EEM.cpp +[ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o -MF CMakeFiles/Descriptors.dir/PBF.cpp.o.d -o CMakeFiles/Descriptors.dir/PBF.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/PBF.cpp +[ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o -MF CMakeFiles/Descriptors.dir/PMI.cpp.o.d -o CMakeFiles/Descriptors.dir/PMI.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/PMI.cpp [ 72%] Linking CXX executable testAbbreviations cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAbbreviations.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -o testAbbreviations ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitAbbreviations.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so -[ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o -MF CMakeFiles/Descriptors.dir/PBF.cpp.o.d -o CMakeFiles/Descriptors.dir/PBF.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/PBF.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 72%] Built target testAbbreviations -[ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o -MF CMakeFiles/Descriptors.dir/PMI.cpp.o.d -o CMakeFiles/Descriptors.dir/PMI.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/PMI.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp:11: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ [ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -MF CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o.d -o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/AUTOCORR3D.cpp [ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o -MF CMakeFiles/Descriptors.dir/RDF.cpp.o.d -o CMakeFiles/Descriptors.dir/RDF.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp [ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Descriptors/MORSE.cpp -[ 72%] Linking CXX executable testMMPA -cd /build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -o testMMPA ../../../lib/libRDKitMMPA.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 72%] Built target testMMPA [ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Descriptors/GETAWAY.cpp [ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o -MF CMakeFiles/Descriptors.dir/WHIM.cpp.o.d -o CMakeFiles/Descriptors.dir/WHIM.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/WHIM.cpp [ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Descriptors/CoulombMat.cpp +[ 73%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp +[ 73%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -MF CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o.d -o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/SubstructMatchCustom.cpp [ 73%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MaeMolSupplier.cpp -[ 73%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Wrap/SDMolSupplier.cpp -[ 73%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMMPA.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o ../../../../lib/libRDKitMMPA.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 73%] Built target rdMMPA -[ 73%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/TDTMolSupplier.cpp -[ 73%] Linking CXX executable testMMFFForceField -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -o testMMFFForceField ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 73%] Built target testMMFFForceField -[ 73%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SmilesMolSupplier.cpp -[ 73%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SmilesWriter.cpp -[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SDWriter.cpp -[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Wrap/TDTWriter.cpp -[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Wrap/PDBWriter.cpp /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/GETAWAY.cpp: In function 'Eigen::MatrixXd RDKit::Descriptors::{anonymous}::GetPinv(const Eigen::MatrixXd&)': /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/GETAWAY.cpp:282:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'Eigen::Index' {aka 'int'} [-Wsign-compare] 282 | for (unsigned int i = 0; i < A.cols(); ++i) { @@ -6570,14 +6574,26 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MaeMolSupplier.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp:13: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp -[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp +[ 73%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Wrap/SDMolSupplier.cpp +[ 73%] Linking CXX shared library ../../../lib/libRDKitFMCS.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFMCS.so.1 -o ../../../lib/libRDKitFMCS.so.1.2022.09.3 CMakeFiles/FMCS.dir/FMCS.cpp.o CMakeFiles/FMCS.dir/Seed.cpp.o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libz.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 73%] 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-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' +[ 73%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/GraphMol/FMCS/testFMCS_Unit.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6592,7 +6608,7 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SDMolSupplier.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MaeMolSupplier.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -6610,10 +6626,16 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/TDTMolSupplier.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SDMolSupplier.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 73%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/TDTMolSupplier.cpp +[ 73%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SmilesMolSupplier.cpp +[ 73%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SmilesWriter.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6632,6 +6654,8 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SDWriter.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6646,43 +6670,7 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SmilesWriter.cpp:11: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SDWriter.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/TDTWriter.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/TDTMolSupplier.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -6700,7 +6688,7 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/PDBWriter.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SmilesWriter.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -6718,13 +6706,40 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp:13: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SDWriter.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 74%] Linking CXX shared library ../../../lib/libRDKitFMCS.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFMCS.so.1 -o ../../../lib/libRDKitFMCS.so.1.2022.09.3 CMakeFiles/FMCS.dir/FMCS.cpp.o CMakeFiles/FMCS.dir/Seed.cpp.o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libz.so +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-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' +[ 74%] Building CXX object Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFMCS_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp +[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Wrap/TDTWriter.cpp +[ 75%] Linking CXX executable testFMCS +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFMCS.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -o testFMCS ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 75%] Built target testFMCS +make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 75%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp +[ 75%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Wrap/PDBWriter.cpp +[ 75%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp +[ 75%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/Descriptors.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDescriptors.so.1 -o ../../../lib/libRDKitDescriptors.so.1.2022.09.3 CMakeFiles/Descriptors.dir/Crippen.cpp.o CMakeFiles/Descriptors.dir/BCUT.cpp.o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o CMakeFiles/Descriptors.dir/MolSurf.cpp.o CMakeFiles/Descriptors.dir/Lipinski.cpp.o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o CMakeFiles/Descriptors.dir/MQN.cpp.o CMakeFiles/Descriptors.dir/Property.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o CMakeFiles/Descriptors.dir/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.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6739,53 +6754,21 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp:13: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 74%] Built target FMCS -make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend -make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend -make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build -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-202209.3/obj-i686-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 74%] Building CXX object Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -[ 74%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/GraphMol/FMCS/testFMCS_Unit.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFMCS_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp -[ 74%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp +[ 75%] Built target Descriptors make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 74%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o +[ 75%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp -[ 74%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.cpp -[ 74%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupCore.cpp -[ 74%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp -[ 74%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupScore.cpp /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'std::string testChEMBL_Txt(const char*, double, const char*)': /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:550:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] 550 | fprintf(fres, "%s;%lu;%.1f;%.4f;%u;%u;%s;", test, mols.size(), th, sec, @@ -6825,10 +6808,6 @@ | | | | long unsigned int std::vector >::size_type {aka unsigned int} | %u -[ 74%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.cpp -[ 75%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6843,266 +6822,347 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp:10: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/TDTWriter.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 75%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolfiles.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolfiles.so CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 75%] Built target rdmolfiles +[ 75%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/PDBWriter.cpp:11: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp:13: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp:13: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 75%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.cpp +[ 75%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupCore.cpp [ 75%] Linking CXX executable FMCStest cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/FMCStest.dir/testFMCS.cpp.o -o FMCStest ../../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 75%] Built target FMCStest -[ 75%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/Descriptors.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDescriptors.so.1 -o ../../../lib/libRDKitDescriptors.so.1.2022.09.3 CMakeFiles/Descriptors.dir/Crippen.cpp.o CMakeFiles/Descriptors.dir/BCUT.cpp.o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o CMakeFiles/Descriptors.dir/MolSurf.cpp.o CMakeFiles/Descriptors.dir/Lipinski.cpp.o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o CMakeFiles/Descriptors.dir/MQN.cpp.o CMakeFiles/Descriptors.dir/Property.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o CMakeFiles/Descriptors.dir/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.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 75%] Built target Descriptors +[ 75%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend -make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend -make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend -make -f Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/depend -make -f Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/depend -make -f Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/depend -make -f Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/depend -make -f Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/depend -make -f Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/DependInfo.cmake --color= -make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DependInfo.cmake --color= -make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 75%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o -MF CMakeFiles/ChemReactions.dir/Reaction.cpp.o.d -o CMakeFiles/ChemReactions.dir/Reaction.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Reaction.cpp +[ 75%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolfiles.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolfiles.so CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 75%] Built target rdmolfiles +make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/test.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/testDescriptors.dir/test.cpp.o -MF CMakeFiles/testDescriptors.dir/test.cpp.o.d -o CMakeFiles/testDescriptors.dir/test.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/test.cpp +[ 75%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o ../../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 75%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupScore.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 75%] Built target rdFMCS +make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -MF CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o.d -o CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testAUTOCORR2D.cpp +[ 75%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.cpp +[ 76%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp +[ 76%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MDLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/MDLParser.cpp +[ 76%] Linking CXX executable testAUTOCORR2D +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR2D.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -o testAUTOCORR2D ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 76%] Built target testAUTOCORR2D +make -f Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 77%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/testATF.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/testATF.dir/testATF.cpp.o -MF CMakeFiles/testATF.dir/testATF.cpp.o.d -o CMakeFiles/testATF.dir/testATF.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testATF.cpp +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-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 77%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/testBCUT.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/testBCUT.dir/testBCUT.cpp.o -MF CMakeFiles/testBCUT.dir/testBCUT.cpp.o.d -o CMakeFiles/testBCUT.dir/testBCUT.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testBCUT.cpp +[ 78%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -MF CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/DaylightParser.cpp +[ 78%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionPickler.cpp +[ 78%] Linking CXX executable testATF +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testATF.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testATF.dir/testATF.cpp.o -o testATF ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 78%] Built target testATF +make -f Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build -make -f Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/testEEM.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/testEEM.cpp.o -MF CMakeFiles/testEEM.dir/testEEM.cpp.o.d -o CMakeFiles/testEEM.dir/testEEM.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testEEM.cpp +make -f Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build +make -f Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build +[ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/testPBF.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/testPBF.cpp.o -MF CMakeFiles/testPBF.dir/testPBF.cpp.o.d -o CMakeFiles/testPBF.dir/testPBF.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testPBF.cpp +[ 78%] Linking CXX executable testDescriptors +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDescriptors.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDescriptors.dir/test.cpp.o -o testDescriptors ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 78%] Linking CXX executable testBCUT +[ 78%] Built target testDescriptors +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testBCUT.dir/link.txt --verbose=1 +make -f Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/DependInfo.cmake --color= +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testBCUT.dir/testBCUT.cpp.o -o testBCUT ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/testRDFcustom.dir/testRDFcustom.cpp.o -MF CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o.d -o CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testRDFcustom.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 78%] Built target testBCUT +make -f Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build -make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build +[ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/testRDF.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/testRDF.dir/testRDF.cpp.o -MF CMakeFiles/testRDF.dir/testRDF.cpp.o.d -o CMakeFiles/testRDF.dir/testRDF.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testRDF.cpp +[ 78%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/RGroupDecomposition.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRGroupDecomposition.so.1 -o ../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitga.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 78%] Built target RGroupDecomposition +make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/testMORSE.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/testMORSE.cpp.o -MF CMakeFiles/testMORSE.dir/testMORSE.cpp.o.d -o CMakeFiles/testMORSE.dir/testMORSE.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testMORSE.cpp +[ 78%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionWriter.cpp +[ 78%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionDepict.cpp +[ 78%] Linking CXX executable testEEM +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEEM.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testEEM.dir/testEEM.cpp.o -o testEEM ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 78%] Built target testEEM +make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/test.cpp.o -[ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/testDescriptors.dir/test.cpp.o -MF CMakeFiles/testDescriptors.dir/test.cpp.o.d -o CMakeFiles/testDescriptors.dir/test.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/test.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/testRDFcustom.dir/testRDFcustom.cpp.o -MF CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o.d -o CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testRDFcustom.cpp -[ 75%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o -[ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -[ 76%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/testATF.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o -MF CMakeFiles/ChemReactions.dir/Reaction.cpp.o.d -o CMakeFiles/ChemReactions.dir/Reaction.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Reaction.cpp -[ 76%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/testPBF.cpp.o -[ 76%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/testBCUT.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -MF CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o.d -o CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testAUTOCORR2D.cpp -[ 76%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/testEEM.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/testATF.dir/testATF.cpp.o -MF CMakeFiles/testATF.dir/testATF.cpp.o.d -o CMakeFiles/testATF.dir/testATF.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testATF.cpp -[ 76%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/testRDF.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/testPBF.cpp.o -MF CMakeFiles/testPBF.dir/testPBF.cpp.o.d -o CMakeFiles/testPBF.dir/testPBF.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testPBF.cpp -[ 76%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/testMORSE.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/testBCUT.dir/testBCUT.cpp.o -MF CMakeFiles/testBCUT.dir/testBCUT.cpp.o.d -o CMakeFiles/testBCUT.dir/testBCUT.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testBCUT.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/testEEM.cpp.o -MF CMakeFiles/testEEM.dir/testEEM.cpp.o.d -o CMakeFiles/testEEM.dir/testEEM.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testEEM.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/testRDF.dir/testRDF.cpp.o -MF CMakeFiles/testRDF.dir/testRDF.cpp.o.d -o CMakeFiles/testRDF.dir/testRDF.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testRDF.cpp -[ 76%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/test3D.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/testMORSE.cpp.o -MF CMakeFiles/testMORSE.dir/testMORSE.cpp.o.d -o CMakeFiles/testMORSE.dir/testMORSE.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testMORSE.cpp +[ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/test3D.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/test3D.cpp.o -MF CMakeFiles/test3D.dir/test3D.cpp.o.d -o CMakeFiles/test3D.dir/test3D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/test3D.cpp -[ 76%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MDLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/MDLParser.cpp -[ 77%] Linking CXX executable testFMCS -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFMCS.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -o testFMCS ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so +[ 78%] Linking CXX executable testPBF +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPBF.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testPBF.dir/testPBF.cpp.o -o testPBF ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 77%] Built target testFMCS +[ 78%] Built target testPBF make -f Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 77%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/testWHIM.cpp.o +[ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/testWHIM.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/testWHIM.dir/testWHIM.cpp.o -MF CMakeFiles/testWHIM.dir/testWHIM.cpp.o.d -o CMakeFiles/testWHIM.dir/testWHIM.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testWHIM.cpp +[ 78%] Linking CXX executable testRDF +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDF.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRDF.dir/testRDF.cpp.o -o testRDF ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 78%] Built target testRDF make -f Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 77%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o +[ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/testGETAWAY.dir/testGETAWAY.cpp.o -MF CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o.d -o CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testGETAWAY.cpp -[ 77%] Linking CXX executable testBCUT -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testBCUT.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testBCUT.dir/testBCUT.cpp.o -o testBCUT ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 78%] Linking CXX executable testMORSE +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMORSE.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMORSE.dir/testMORSE.cpp.o -o testMORSE ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 78%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 77%] Built target testBCUT +[ 78%] Built target testMORSE make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 77%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o +[ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -MF CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o.d -o CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testAUTOCORR3D.cpp -[ 77%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o ../../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 79%] Linking CXX executable testRDFcustom +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDFcustom.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -o testRDFcustom ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 77%] Built target rdFMCS +[ 79%] Built target testRDFcustom make -f Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' -[ 77%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o +[ 79%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/testCoulombMat.dir/testCoulombMat.cpp.o -MF CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o.d -o CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testCoulombMat.cpp -[ 77%] Linking CXX executable testATF -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testATF.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testATF.dir/testATF.cpp.o -o testATF ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 79%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionUtils.cpp +[ 79%] Linking CXX executable testWHIM +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testWHIM.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testWHIM.dir/testWHIM.cpp.o -o testWHIM ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 77%] Built target testATF +[ 79%] Built target testWHIM make -f Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' -[ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o +[ 80%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/GraphMol/Descriptors/catch_tests.cpp -[ 78%] Linking CXX executable testEEM -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEEM.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testEEM.dir/testEEM.cpp.o -o testEEM ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 80%] Linking CXX executable test3D +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/test3D.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/test3D.dir/test3D.cpp.o -o test3D ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 78%] Built target testEEM +[ 80%] Built target test3D make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' -[ 78%] Building CXX object Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o +[ 80%] Building CXX object Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDescriptors_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o -MF CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o.d -o CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp -[ 78%] Linking CXX executable testMORSE -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMORSE.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMORSE.dir/testMORSE.cpp.o -o testMORSE ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 80%] Linking CXX executable testGETAWAY +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGETAWAY.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o -o testGETAWAY ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 78%] Built target testMORSE +[ 80%] Built target testGETAWAY make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 78%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o +[ 80%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -MF CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o.d -o CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/testMolAlign.cpp -[ 78%] Linking CXX executable testRDF -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDF.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRDF.dir/testRDF.cpp.o -o testRDF ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 78%] Linking CXX executable testAUTOCORR2D -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR2D.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -o testAUTOCORR2D ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 80%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/MoleculeParser.cpp +[ 80%] Linking CXX executable testAUTOCORR3D +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR3D.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -o testAUTOCORR3D ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 78%] Built target testRDF +[ 80%] Built target testAUTOCORR3D make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 78%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o +[ 80%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -MF CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o.d -o CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/testO3AAlign.cpp +[ 80%] Linking CXX executable testCoulombMat +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -o testCoulombMat ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 78%] Built target testAUTOCORR2D +[ 80%] Built target testCoulombMat make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 78%] Building CXX object Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o +[ 80%] Building CXX object Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolAlign_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -MF CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o.d -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp -[ 79%] Linking CXX executable testRDFcustom -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDFcustom.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -o testRDFcustom ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 79%] Built target testRDFcustom -make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 79%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o -MF CMakeFiles/MolHash.dir/hashfunctions.cpp.o.d -o CMakeFiles/MolHash.dir/hashfunctions.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/hashfunctions.cpp -[ 79%] Linking CXX executable testPBF -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPBF.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testPBF.dir/testPBF.cpp.o -o testPBF ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 79%] Built target testPBF -[ 80%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o -MF CMakeFiles/MolHash.dir/normalize.cpp.o.d -o CMakeFiles/MolHash.dir/normalize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/normalize.cpp -[ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -MF CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/DaylightParser.cpp -[ 81%] Linking CXX executable test3D -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/test3D.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/test3D.dir/test3D.cpp.o -o test3D ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 81%] Built target test3D -[ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionPickler.cpp -[ 81%] Linking CXX executable testWHIM -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testWHIM.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testWHIM.dir/testWHIM.cpp.o -o testWHIM ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 81%] Built target testWHIM -[ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionWriter.cpp -[ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionDepict.cpp +[ 80%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/ChemReactions/ReactionRunner.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7120,33 +7180,21 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 81%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/RGroupDecomposition.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRGroupDecomposition.so.1 -o ../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitga.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 81%] Linking CXX executable testGETAWAY -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGETAWAY.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o -o testGETAWAY ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 81%] 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-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 81%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -MF CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o.d -o CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp +[ 80%] Linking CXX executable descriptorsTestCatch +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/descriptorsTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -o descriptorsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 80%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/PreprocessRxn.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 81%] Built target testGETAWAY -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/depend +[ 80%] Built target descriptorsTestCatch +make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build +make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 81%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -MF CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o.d -o CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/testRGroupInternals.cpp +[ 80%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o -MF CMakeFiles/MolHash.dir/hashfunctions.cpp.o.d -o CMakeFiles/MolHash.dir/hashfunctions.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/hashfunctions.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7165,39 +7213,6 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 81%] Linking CXX executable testCoulombMat -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -o testCoulombMat ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 81%] Built target testCoulombMat -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 81%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -MF CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o.d -o CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/catch_rgd.cpp -[ 81%] Linking CXX executable testAUTOCORR3D -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR3D.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -o testAUTOCORR3D ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 81%] Built target testAUTOCORR3D -make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 81%] Building CXX object Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -MF CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o.d -o CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp -[ 81%] Linking CXX executable descriptorsTestCatch -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/descriptorsTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -o descriptorsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 81%] Built target descriptorsTestCatch -[ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp: In function 'RDKit::MolAlign::PyO3A* RDKit::MolAlign::getCrippenO3A(RDKit::ROMol&, RDKit::ROMol&, boost::python::list, boost::python::list, int, int, bool, unsigned int, unsigned int, boost::python::list, boost::python::list)': /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:431:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] 431 | (python::len(prbCrippenContribs) == prbNAtoms)) { @@ -7212,38 +7227,98 @@ /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:522:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] 522 | (python::len(refCrippenContribs) == refNAtoms)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionUtils.cpp -[ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/MoleculeParser.cpp -[ 81%] Linking CXX shared library ../../../lib/libRDKitMolHash.so +[ 80%] Linking CXX executable testMolAlign +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -o testMolAlign ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 80%] Built target testMolAlign +[ 81%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o -MF CMakeFiles/MolHash.dir/normalize.cpp.o.d -o CMakeFiles/MolHash.dir/normalize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/normalize.cpp +[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/ChemReactions/SanitizeRxn.cpp +[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/ChemReactions/PNGParser.cpp +[ 82%] Linking CXX executable testO3AAlign +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -o testO3AAlign ../../../lib/libRDKitO3AAlign.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 82%] Built target testO3AAlign +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-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 82%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -MF CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o.d -o CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp +[ 82%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o ../../../../lib/libRDKitO3AAlign.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 82%] Built target rdMolAlign +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 82%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -MF CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o.d -o CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/testRGroupInternals.cpp +[ 82%] Linking CXX shared library ../../../lib/libRDKitMolHash.so cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolHash.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolHash.so.1 -o ../../../lib/libRDKitMolHash.so.1.2022.09.3 CMakeFiles/MolHash.dir/hashfunctions.cpp.o CMakeFiles/MolHash.dir/normalize.cpp.o ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2022.09.3 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 81%] Built target MolHash +[ 82%] Built target MolHash +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 82%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -MF CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o.d -o CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/catch_rgd.cpp +[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/CDXMLParser.cpp +[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp +[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp +[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp +make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 82%] Building CXX object Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -MF CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o.d -o CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp +[ 82%] Linking CXX executable rgroupCatchTests +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/rgroupCatchTests.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -o rgroupCatchTests ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl ../../../lib/libRDKitga.so.1.2022.09.3 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 82%] Built target rgroupCatchTests make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 81%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o +[ 82%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/catch_tests.cpp -[ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/ChemReactions/ReactionRunner.cpp -[ 81%] Linking CXX executable testMolAlign -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -o testMolAlign ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 82%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDescriptors.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolDescriptors.so CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 81%] Built target testMolAlign +[ 82%] Built target rdMolDescriptors 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' -[ 81%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o +[ 82%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolHash_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, @@ -7263,23 +7338,6 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/PreprocessRxn.cpp -[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/ChemReactions/SanitizeRxn.cpp -[ 82%] Linking CXX executable testO3AAlign -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -o testO3AAlign ../../../lib/libRDKitO3AAlign.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/ChemReactions/PNGParser.cpp -[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/CDXMLParser.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 82%] Built target testO3AAlign -[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp -[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7298,144 +7356,128 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 82%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o ../../../../lib/libRDKitO3AAlign.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 82%] Built target rdMolAlign -[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp -[ 82%] Linking CXX executable rgroupCatchTests -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/rgroupCatchTests.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -o rgroupCatchTests ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl ../../../lib/libRDKitga.so.1.2022.09.3 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 82%] Built target rgroupCatchTests -[ 83%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolHash.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o ../../../../lib/libRDKitMolHash.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 83%] Built target rdMolHash -[ 83%] Linking CXX executable molHashCatchTest -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/molHashCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -o molHashCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolHash.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 83%] Built target molHashCatchTest -[ 83%] Linking CXX executable testDescriptors -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDescriptors.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDescriptors.dir/test.cpp.o -o testDescriptors ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 83%] Built target testDescriptors -[ 83%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitga.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 83%] Built target rdRGroupDecomposition -[ 83%] Linking CXX executable testRGroupDecompInternals +[ 82%] Linking CXX executable testRGroupDecompInternals cd /build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -o testRGroupDecompInternals ../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl ../../../lib/libRDKitga.so.1.2022.09.3 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 83%] Built target testRGroupDecompInternals -[ 83%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so +[ 82%] Built target testRGroupDecompInternals +[ 82%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemReactions.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemReactions.so.1 -o ../../../lib/libRDKitChemReactions.so.1.2022.09.3 CMakeFiles/ChemReactions.dir/Reaction.cpp.o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 83%] Built target ChemReactions +[ 82%] Built target ChemReactions make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend -make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend -make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend -make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend -make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend -make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake --color= cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake --color= -make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend -make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build +[ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -MF CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o.d -o CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp +[ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o +[ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o -MF CMakeFiles/testReaction.dir/testReaction.cpp.o.d -o CMakeFiles/testReaction.dir/testReaction.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testReaction.cpp +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -MF CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o.d -o CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp +[ 84%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolHash.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o ../../../../lib/libRDKitMolHash.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build +[ 84%] Built target rdMolHash +make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp +[ 84%] Linking CXX executable molHashCatchTest +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/molHashCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -o molHashCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolHash.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 84%] Built target molHashCatchTest +make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 84%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -MF CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o.d -o CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp +In file included from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp:10: +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp: In function 'void C_A_T_C_H_T_E_S_T_72()': +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp:1257:63: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 1257 | CHECK(mol->getProp("CDX_REAGENT_ID") == i++); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp:1264:63: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 1264 | CHECK(mol->getProp("CDX_PRODUCT_ID") == i++); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +[ 84%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitga.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 84%] Built target rdRGroupDecomposition +make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build +make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 84%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -MF CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o.d -o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/MolStandardize.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 84%] Linking CXX executable testRGroupDecomp +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl ../../../lib/libRDKitga.so.1.2022.09.3 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build +[ 84%] Built target testRGroupDecomp +[ 84%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -MF CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o.d -o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp +[ 84%] Linking CXX executable testReactionFingerprints +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReactionFingerprints.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -o testReactionFingerprints ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build +[ 84%] Built target testReactionFingerprints +make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o -[ 83%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -[ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -[ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -MF CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o.d -o CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp -[ 83%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o -[ 83%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -[ 83%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -MF CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o.d -o CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp -[ 84%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -[ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Wrap/rdmolops.cpp -[ 84%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o -MF CMakeFiles/testReaction.dir/testReaction.cpp.o.d -o CMakeFiles/testReaction.dir/testReaction.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testReaction.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Wrap/MolOps.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -MF CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o.d -o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/MolStandardize.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -MF CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o.d -o CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -MF CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o.d -o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp -[ 85%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -MF CMakeFiles/MolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Metal.cpp -[ 85%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -MF CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o.d -o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ChiralityOps.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDeprotect_EXPORTS -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o -MF CMakeFiles/Deprotect.dir/Deprotect.cpp.o.d -o CMakeFiles/Deprotect.dir/Deprotect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Deprotect.cpp -[ 85%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o +[ 84%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.cpp -[ 85%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -MF CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o.d -o CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.cpp -[ 85%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDescriptors.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolDescriptors.so CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 85%] Built target rdMolDescriptors -[ 85%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolStandardize/Normalize.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7453,6 +7495,19 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 84%] Linking CXX executable testEnumeration +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -o testEnumeration ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 84%] Built target testEnumeration +make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 84%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDeprotect_EXPORTS -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o -MF CMakeFiles/Deprotect.dir/Deprotect.cpp.o.d -o CMakeFiles/Deprotect.dir/Deprotect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Deprotect.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7460,24 +7515,34 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ChiralityOps.cpp:10: + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.h:24, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolPickler.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:34: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 85%] Linking CXX executable testRGroupDecomp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl ../../../lib/libRDKitga.so.1.2022.09.3 +[ 84%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -MF CMakeFiles/MolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Metal.cpp +[ 85%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp +[ 85%] Linking CXX shared library ../../../lib/libRDKitDeprotect.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/Deprotect.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDeprotect.so.1 -o ../../../lib/libRDKitDeprotect.so.1.2022.09.3 CMakeFiles/Deprotect.dir/Deprotect.cpp.o ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDeprotect.so.1.2022.09.3 ../../../lib/libRDKitDeprotect.so.1 ../../../lib/libRDKitDeprotect.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 85%] Built target testRGroupDecomp -[ 86%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o -MF CMakeFiles/MolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/MolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Validate.cpp +[ 85%] Built target Deprotect +make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' +[ 85%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Wrap/rdmolops.cpp +[ 85%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolStandardize/Normalize.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7491,10 +7556,26 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32: + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdmolops.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 85%] Linking CXX executable rxnTestCatch +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/rxnTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -o rxnTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 85%] Built target rxnTestCatch +make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 85%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -MF CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o.d -o CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.cpp +[ 85%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/Wrap/MolOps.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7513,9 +7594,34 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 85%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp +[ 85%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp +In copy constructor 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]', + inlined from 'PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:14: +/usr/include/boost/smart_ptr/shared_ptr.hpp:416:66: 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] + 416 | shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn ) + | ~~^~ +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp: In function 'PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]': +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:30: note: '' declared here + 129 | ROMOL_SPTR react = python::extract(reactant); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/shared_ptr.hpp:17: +In copy constructor 'boost::detail::shared_count::shared_count(const boost::detail::shared_count&)', + inlined from 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]' at /usr/include/boost/smart_ptr/shared_ptr.hpp:416:72, + inlined from 'PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:14: +/usr/include/boost/smart_ptr/detail/shared_count.hpp:438:67: warning: '((const boost::detail::shared_count*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)))[1].boost::detail::shared_count::pi_' may be used uninitialized [-Wmaybe-uninitialized] + 438 | shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_) + | ~~^~~ +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp: In function 'PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]': +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:30: note: '' declared here + 129 | ROMOL_SPTR react = python::extract(reactant); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 86%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o -MF CMakeFiles/MolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/MolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Validate.cpp +[ 86%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -MF CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o.d -o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/PositionVariation.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7523,25 +7629,43 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdmolops.cpp:12: + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.h:24, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:30, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp:10: -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp: In function 'void C_A_T_C_H_T_E_S_T_72()': -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp:1257:63: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 1257 | CHECK(mol->getProp("CDX_REAGENT_ID") == i++); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp:1264:63: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 1264 | CHECK(mol->getProp("CDX_PRODUCT_ID") == i++); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +[ 86%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -MF CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o.d -o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/LinkNode.cpp +[ 86%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -MF CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/AtomSymbol.cpp +[ 86%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o -MF CMakeFiles/MolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/MolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Charge.cpp +[ 87%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdChemReactions.so CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawAnnotation.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 87%] Built target rdChemReactions +[ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolDraw2D/DrawMol.cpp +[ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawMolMCH.cpp +[ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawShape.cpp +[ 87%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -MF CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o.d -o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/RepeatUnit.cpp +[ 87%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -MF CMakeFiles/MolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Tautomer.cpp +[ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -MF CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o.d -o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ChiralityOps.cpp +[ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawText.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawText.cpp +[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextNotFT.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7549,62 +7673,69 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.h:24, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolPickler.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:34: + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ChiralityOps.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 86%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o -MF CMakeFiles/MolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/MolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Charge.cpp -[ 86%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -MF CMakeFiles/MolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Tautomer.cpp -[ 86%] Linking CXX shared library ../../../lib/libRDKitDeprotect.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/Deprotect.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDeprotect.so.1 -o ../../../lib/libRDKitDeprotect.so.1.2022.09.3 CMakeFiles/Deprotect.dir/Deprotect.cpp.o ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so -[ 86%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -MF CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o.d -o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/PositionVariation.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDeprotect.so.1.2022.09.3 ../../../lib/libRDKitDeprotect.so.1 ../../../lib/libRDKitDeprotect.so +[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextSVG.cpp +[ 89%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolEnumerator.so.1 -o ../../../lib/libRDKitMolEnumerator.so.1.2022.09.3 CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2022.09.3 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 86%] Built target Deprotect +[ 89%] Built target MolEnumerator 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/DependInfo.cmake --color= +[ 89%] Linking CXX executable testReaction make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 86%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o +[ 89%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -MF CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o.d -o CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/deprotectTest.cpp -[ 86%] Linking CXX executable testReactionFingerprints -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReactionFingerprints.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -o testReactionFingerprints ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 86%] Built target testReactionFingerprints +[ 89%] Built target testReaction make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 87%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o +[ 90%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -MF CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o.d -o CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Wrap/rdDeprotect.cpp -[ 87%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o -MF CMakeFiles/MolStandardize.dir/Fragment.cpp.o.d -o CMakeFiles/MolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Fragment.cpp -[ 87%] Linking CXX executable testEnumeration -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -o testEnumeration ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 87%] Built target testEnumeration -[ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp -[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp -[ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp -[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp +[ 90%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolops.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolops.so CMakeFiles/rdmolops.dir/rdmolops.cpp.o CMakeFiles/rdmolops.dir/MolOps.cpp.o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 90%] Built target rdmolops +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-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 90%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -MF CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o.d -o CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/enumerator_catch.cpp +[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DJS.cpp +[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextJS.cpp +[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DCairo.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7623,27 +7754,29 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp -[ 88%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o +[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextCairo.cpp +[ 90%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -MF CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o.d -o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp -[ 88%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -MF CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o.d -o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/LinkNode.cpp -[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp -[ 88%] Linking CXX executable deprotectTest +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp +[ 90%] Linking CXX executable deprotectTest cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/deprotectTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -o deprotectTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDeprotect.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 88%] Built target deprotectTest -[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp -[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp -[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp -[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.cpp +[ 90%] Built target deprotectTest +make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' +[ 90%] Building CXX object Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolEnumerator_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -MF CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o.d -o CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp +[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextFT.cpp +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7662,53 +7795,6 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp -In copy constructor 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]', - inlined from 'PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:14: -/usr/include/boost/smart_ptr/shared_ptr.hpp:416:66: 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] - 416 | shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn ) - | ~~^~ -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp: In function 'PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]': -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:30: note: '' declared here - 129 | ROMOL_SPTR react = python::extract(reactant); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/shared_ptr.hpp:17: -In copy constructor 'boost::detail::shared_count::shared_count(const boost::detail::shared_count&)', - inlined from 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]' at /usr/include/boost/smart_ptr/shared_ptr.hpp:416:72, - inlined from 'PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:14: -/usr/include/boost/smart_ptr/detail/shared_count.hpp:438:67: warning: '((const boost::detail::shared_count*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)))[1].boost::detail::shared_count::pi_' may be used uninitialized [-Wmaybe-uninitialized] - 438 | shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_) - | ~~^~~ -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp: In function 'PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]': -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:30: note: '' declared here - 129 | ROMOL_SPTR react = python::extract(reactant); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp -[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp -[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp -[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -MF CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/AtomSymbol.cpp -[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp -[ 89%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -MF CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o.d -o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/RepeatUnit.cpp -[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawAnnotation.cpp -[ 89%] Linking CXX executable rxnTestCatch -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/rxnTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -o rxnTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so -[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolDraw2D/DrawMol.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 89%] Built target rxnTestCatch -[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawMolMCH.cpp -[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawShape.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7716,125 +7802,213 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.h:24, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:30, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp:10: + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawText.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawText.cpp -[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextNotFT.cpp -[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextSVG.cpp -[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DJS.cpp -[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextJS.cpp -[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DCairo.cpp -[ 90%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDeprotect.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDeprotect.so CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o ../../../../lib/libRDKitDeprotect.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 90%] Built target rdDeprotect -[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextCairo.cpp -[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextFT.cpp [ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolDraw2D/DrawTextFTSVG.cpp +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp [ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextFTJS.cpp [ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolDraw2D/DrawTextFTCairo.cpp -[ 91%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so +[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp +[ 91%] Linking CXX executable testMolEnumerator +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolEnumerator.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -o testMolEnumerator ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolEnumerator.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 91%] Built target testMolEnumerator +[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp +[ 92%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDeprotect.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDeprotect.so CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o ../../../../lib/libRDKitDeprotect.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 92%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolEnumerator.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolEnumerator.so CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o ../../../../lib/libRDKitMolEnumerator.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 92%] Built target rdDeprotect +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp +[ 92%] Built target rdMolEnumerator +[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.cpp +[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp +[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp +[ 92%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolDraw2D.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolDraw2D.so.1 -o ../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o ../../../lib/libRDKitChemReactions.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libfreetype.so ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libcairo.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 92%] Built target MolDraw2D +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -MF CMakeFiles/moldraw2DTest1.dir/test1.cpp.o.d -o CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/test1.cpp +[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp +[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/catch_tests.cpp +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -MF CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o.d -o CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/rxn_test1.cpp +make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 92%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDraw2D_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -MF CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o.d -o CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:11: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 92%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolStandardize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolStandardize.so.1 -o ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o CMakeFiles/MolStandardize.dir/Metal.cpp.o CMakeFiles/MolStandardize.dir/Normalize.cpp.o CMakeFiles/MolStandardize.dir/Validate.cpp.o CMakeFiles/MolStandardize.dir/Charge.cpp.o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o CMakeFiles/MolStandardize.dir/Fragment.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so /usr/lib/i386-linux-gnu/libboost_serialization.so cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 91%] Built target MolStandardize +[ 92%] Built target MolStandardize make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend +make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -MF CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o.d -o CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/testNormalize.cpp +[ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o +[ 93%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o -MF CMakeFiles/molStandardizeTest.dir/test1.cpp.o.d -o CMakeFiles/molStandardizeTest.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/test1.cpp -[ 91%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_TAUTOMERQUERY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTautomerQuery_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -MF CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o.d -o CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery/TautomerQuery.cpp -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-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake --color= +[ 93%] Linking CXX executable moldraw2DRxnTest1 +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DRxnTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -o moldraw2DRxnTest1 ../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libcairo.so /usr/lib/i386-linux-gnu/libfreetype.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -MF CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o.d -o CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/testNormalize.cpp -[ 92%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolops.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolops.so CMakeFiles/rdmolops.dir/rdmolops.cpp.o CMakeFiles/rdmolops.dir/MolOps.cpp.o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 93%] Built target moldraw2DRxnTest1 make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o +[ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o -MF CMakeFiles/molValidateTest.dir/testValidate.cpp.o.d -o CMakeFiles/molValidateTest.dir/testValidate.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/testValidate.cpp -[ 92%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolEnumerator.so.1 -o ../../../lib/libRDKitMolEnumerator.so.1.2022.09.3 CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so +[ 93%] Linking CXX executable molNormalizeTest +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molNormalizeTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -o molNormalizeTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 92%] Built target rdmolops +[ 93%] Built target molNormalizeTest 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o +[ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o -MF CMakeFiles/molChargeTest.dir/testCharge.cpp.o.d -o CMakeFiles/molChargeTest.dir/testCharge.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/testCharge.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2022.09.3 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so +[ 93%] Linking CXX executable molValidateTest +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molValidateTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molValidateTest.dir/testValidate.cpp.o -o molValidateTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 92%] Built target MolEnumerator +[ 93%] Built target molValidateTest 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o +[ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -MF CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o.d -o CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/testTautomer.cpp +[ 94%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTautomerQuery.so.1 -o ../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 94%] Built target TautomerQuery 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-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o +[ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -MF CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o.d -o CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/test2.cpp +[ 94%] Linking CXX executable molStandardizeTest +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molStandardizeTest.dir/test1.cpp.o -o molStandardizeTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 94%] Built target molStandardizeTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o +[ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -MF CMakeFiles/molFragmentTest.dir/testFragment.cpp.o.d -o CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/testFragment.cpp -[ 94%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdChemReactions.so CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 94%] Linking CXX executable moldraw2DTest1 +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 ../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libcairo.so /usr/lib/i386-linux-gnu/libfreetype.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 94%] Built target moldraw2DTest1 make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/DependInfo.cmake --color= @@ -7843,73 +8017,45 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/catch_tests.cpp +[ 95%] Linking CXX executable molChargeTest +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molChargeTest.dir/testCharge.cpp.o -o molChargeTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 94%] Built target rdChemReactions +[ 95%] Built target molChargeTest make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend -make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build -make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 95%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -[ 95%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SCAFFOLDNETWORK_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DScaffoldNetwork_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -MF CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o.d -o CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -MF CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp -[ 95%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolStandardize/Wrap/Validate.cpp -[ 95%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Charge.cpp -[ 95%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp:10: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ [ 95%] Linking CXX executable molStandardizeSmallTest cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeSmallTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -o molStandardizeSmallTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 95%] Built target molStandardizeSmallTest -make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend +make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build +make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 95%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -MF CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o.d -o CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/enumerator_catch.cpp -[ 96%] Linking CXX executable molChargeTest -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molChargeTest.dir/testCharge.cpp.o -o molChargeTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 96%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SCAFFOLDNETWORK_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DScaffoldNetwork_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -MF CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o.d -o CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp +[ 96%] Linking CXX executable molFragmentTest +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molFragmentTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -o molFragmentTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 96%] Built target molChargeTest -make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend +[ 96%] Built target molFragmentTest +make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build +make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 96%] Building CXX object Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolEnumerator_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -MF CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o.d -o CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp +[ 96%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery/catch_tests.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7920,27 +8066,58 @@ from /usr/include/boost/smart_ptr.hpp:19, from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Validate.cpp:10: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 96%] Linking CXX executable molNormalizeTest -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molNormalizeTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -o molNormalizeTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 96%] Linking CXX executable molFragmentTest -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molFragmentTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -o molFragmentTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 96%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcairo.so /usr/lib/i386-linux-gnu/libfreetype.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 96%] Built target molNormalizeTest -[ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp +[ 96%] Built target rdMolDraw2D +make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 96%] Built target molFragmentTest -[ 97%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Metal.cpp +make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 96%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdTautomerQuery_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -MF CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o.d -o CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp +[ 96%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitScaffoldNetwork.so.1 -o ../../../lib/libRDKitScaffoldNetwork.so.1.2022.09.3 CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2022.09.3 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 96%] Built target ScaffoldNetwork +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 96%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -MF CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp +[ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolStandardize/Wrap/Validate.cpp +[ 96%] Linking CXX executable tautomerQueryTestCatch +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/tautomerQueryTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -o tautomerQueryTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 96%] Built target tautomerQueryTestCatch +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-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' +[ 97%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -MF CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o.d -o CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/catch_tests.cpp +[ 98%] Linking CXX executable moldraw2DTestCatch +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 ../../../lib/libRDKitCIPLabeler.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcairo.so /usr/lib/i386-linux-gnu/libfreetype.so ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7951,48 +8128,30 @@ from /usr/include/boost/smart_ptr.hpp:19, from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Charge.cpp:10: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 97%] Linking CXX executable molValidateTest -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molValidateTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molValidateTest.dir/testValidate.cpp.o -o molValidateTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 97%] Built target molValidateTest -[ 97%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp -[ 97%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTautomerQuery.so.1 -o ../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 97%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitScaffoldNetwork.so.1 -o ../../../lib/libRDKitScaffoldNetwork.so.1.2022.09.3 CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so +[ 98%] Linking CXX executable molStandardizeCatchTest +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -o molStandardizeCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2022.09.3 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so -[ 97%] Built target TautomerQuery -make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend +[ 98%] Built target moldraw2DTestCatch +make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 97%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery/catch_tests.cpp -[ 97%] Built target ScaffoldNetwork -make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/depend +make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/DependInfo.cmake --color= +[ 98%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdScaffoldNetwork_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -MF CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o.d -o CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 97%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdTautomerQuery_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -MF CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o.d -o CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp +[ 98%] Built target molStandardizeCatchTest +[ 98%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -MF CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/PatternFactory.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8003,28 +8162,20 @@ from /usr/include/boost/smart_ptr.hpp:19, from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp:10: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Validate.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 97%] Linking CXX executable molStandardizeTest -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molStandardizeTest.dir/test1.cpp.o -o molStandardizeTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 97%] Built target molStandardizeTest -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake --color= +[ 98%] Linking CXX executable molTautomerTest +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTautomerTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -o molTautomerTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 97%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -MF CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp -[ 97%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -MF CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/PatternFactory.cpp +[ 98%] Built target molTautomerTest +[ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Charge.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8039,7 +8190,7 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -8053,13 +8204,26 @@ from /usr/include/boost/smart_ptr.hpp:19, from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp:10: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Charge.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp +[ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp +[ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdTautomerQuery.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdTautomerQuery.so CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o ../../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[ 99%] Built target rdTautomerQuery +[100%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Metal.cpp +[100%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8070,13 +8234,23 @@ from /usr/include/boost/smart_ptr.hpp:19, from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Metal.cpp:10: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[100%] Linking CXX executable testScaffoldNetwork +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/testScaffoldNetwork.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -o testScaffoldNetwork ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitScaffoldNetwork.so.1.2022.09.3 ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[100%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdScaffoldNetwork.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o ../../../../lib/libRDKitScaffoldNetwork.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[100%] Built target rdScaffoldNetwork +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[100%] Built target testScaffoldNetwork In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8084,40 +8258,16 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/object/class.hpp:9, - from /usr/include/boost/python/class.hpp:13, - from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:9, - from /usr/include/boost/python/suite/indexing/map_indexing_suite.hpp:9, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp:11: -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Metal.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -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-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3/obj-i686-linux-gnu' -[ 98%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -MF CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o.d -o CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/catch_tests.cpp -make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 98%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdScaffoldNetwork_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -MF CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o.d -o CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp -[ 98%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolDraw2D.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolDraw2D.so.1 -o ../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o ../../../lib/libRDKitChemReactions.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libfreetype.so ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libcairo.so +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8128,48 +8278,43 @@ from /usr/include/boost/smart_ptr.hpp:19, from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so +[100%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructLibrary.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructLibrary.so.1 -o ../../../lib/libRDKitSubstructLibrary.so.1.2022.09.3 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o ../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2022.09.3 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 98%] Built target MolDraw2D -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend +[100%] Built target SubstructLibrary +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/depend +make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 98%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -MF CMakeFiles/moldraw2DTest1.dir/test1.cpp.o.d -o CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/test1.cpp -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 98%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/catch_tests.cpp -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake --color= +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 98%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -MF CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o.d -o CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/rxn_test1.cpp -make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend +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-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 98%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDraw2D_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -MF CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o.d -o CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp +make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[100%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp +[100%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o +[100%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/GraphMol/SubstructLibrary/catch_tests.cpp +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8181,28 +8326,19 @@ from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp:11: + from /usr/include/boost/python/object/class.hpp:9, + from /usr/include/boost/python/class.hpp:13, + from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:9, + from /usr/include/boost/python/suite/indexing/map_indexing_suite.hpp:9, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp:11: +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 98%] Linking CXX executable molStandardizeCatchTest -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -o molStandardizeCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 98%] Linking CXX executable tautomerQueryTestCatch -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/tautomerQueryTestCatch.dir/link.txt --verbose=1 -[ 98%] Built target molStandardizeCatchTest -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -o tautomerQueryTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so -[ 98%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolEnumerator.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolEnumerator.so CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o ../../../../lib/libRDKitMolEnumerator.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 98%] Built target rdMolEnumerator -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 98%] Built target tautomerQueryTestCatch +[100%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8217,77 +8353,10 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp:33: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 98%] Linking CXX executable testMolEnumerator -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolEnumerator.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -o testMolEnumerator ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolEnumerator.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 98%] Linking CXX executable molTautomerTest -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTautomerTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -o molTautomerTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 98%] Built target molTautomerTest -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 98%] Built target testMolEnumerator -[ 98%] Linking CXX executable moldraw2DRxnTest1 -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DRxnTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -o moldraw2DRxnTest1 ../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libcairo.so /usr/lib/i386-linux-gnu/libfreetype.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 98%] Built target moldraw2DRxnTest1 -[ 98%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolStandardize.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o ../../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 98%] Built target rdMolStandardize -[ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdTautomerQuery.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdTautomerQuery.so CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o ../../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 99%] Built target rdTautomerQuery -[ 99%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdScaffoldNetwork.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o ../../../../lib/libRDKitScaffoldNetwork.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 99%] Built target rdScaffoldNetwork -[ 99%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructLibrary.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructLibrary.so.1 -o ../../../lib/libRDKitSubstructLibrary.so.1.2022.09.3 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o ../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so -[ 99%] Linking CXX executable testScaffoldNetwork -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/testScaffoldNetwork.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -o testScaffoldNetwork ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitScaffoldNetwork.so.1.2022.09.3 ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2022.09.3 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 99%] Built target SubstructLibrary -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/depend -make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake --color= -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build -make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 99%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -[ 99%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -[ 99%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp -[ 99%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -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-202209.3/Code/GraphMol/SubstructLibrary/catch_tests.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -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-202209.3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 99%] Built target testScaffoldNetwork In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8303,40 +8372,19 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp:33: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 99%] Linking CXX executable testReaction -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 99%] Built target testReaction -[ 99%] Linking CXX executable substructLibraryCatchTest +[100%] Linking CXX executable substructLibraryCatchTest cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -o substructLibraryCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2022.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libboost_serialization.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 99%] Built target substructLibraryCatchTest -[ 99%] Linking CXX executable substructLibraryTest +[100%] Built target substructLibraryCatchTest +[100%] Linking CXX executable substructLibraryTest cd /build/reproducible-path/rdkit-202209.3/obj-i686-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-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -o substructLibraryTest ../../../lib/libRDKitSubstructLibrary.so.1.2022.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' +[100%] Built target substructLibraryTest /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp: In member function 'unsigned int RDKit::SubstructLibraryWrap::countMatches(const Query&, unsigned int, unsigned int, bool, bool, bool, int) const [with Query = RDKit::MolBundle]': /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp:153:16: warning: infinite recursion detected [-Winfinite-recursion] 153 | unsigned int countMatches(const Query &query, unsigned int startIdx, @@ -8364,23 +8412,11 @@ | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 | numThreads); | ~~~~~~~~~~~ +[100%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so +cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolStandardize.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o ../../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 99%] Built target substructLibraryTest -[ 99%] Linking CXX executable moldraw2DTest1 -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 ../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/i386-linux-gnu/libcairo.so /usr/lib/i386-linux-gnu/libfreetype.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 99%] Built target moldraw2DTest1 -[ 99%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcairo.so /usr/lib/i386-linux-gnu/libfreetype.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[ 99%] Built target rdMolDraw2D -[100%] Linking CXX executable moldraw2DTestCatch -cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 ../../../lib/libRDKitCIPLabeler.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcairo.so /usr/lib/i386-linux-gnu/libfreetype.so ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -[100%] Built target moldraw2DTestCatch +[100%] Built target rdMolStandardize [100%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSubstructLibrary.so CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o ../../../../lib/libRDKitSubstructLibrary.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libz.so ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl @@ -8605,69 +8641,69 @@ Searching for files to exclude Searching INPUT for files to process... Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/tutorial Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/libs -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/UFF -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/GenericGroups -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Qt -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Qt/Demo -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Fonts -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DetermineBonds -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/StructChecker -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/libs +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DetermineBonds Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/GenericGroups +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Fonts +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Qt +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Qt/Demo Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/StructChecker +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/Catalogs Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/DataStructs Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/Query Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/ML -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/ML/Data Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/ML/Cluster Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/ML/Cluster/Murtagh Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/ML/Data Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/DataManip Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/DataManip/MetricMatrixCalc Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers @@ -9701,6 +9737,8 @@ Generating code for file RegisterDescriptor.h... Generating code for file USRDescriptor.h... Generating code for file WHIM.h... +Generating code for file details.h... +Generating code for file details.h... Generating code for file DetermineBonds.h... Generating code for file BoundsMatrixBuilder.h... Generating code for file Embedder.h... @@ -9811,8 +9849,6 @@ Generating code for file mf.h... Generating code for file MolHash.h... Generating code for file nmmolhash.h... -Generating code for file details.h... -Generating code for file details.h... Generating code for file MolInterchange.h... Generating code for file MolOps.h... Generating code for file MolPickler.h... @@ -9827,6 +9863,8 @@ Generating code for file Metal.h... Generating code for file MolStandardize.h... Generating code for file Normalize.h... +Generating code for file Tautomer.h... +Generating code for file Tautomer.h... Generating code for file TautomerCatalogEntry.h... Generating code for file TautomerCatalogParams.h... Generating code for file TautomerCatalogUtils.h... @@ -9880,8 +9918,6 @@ Generating code for file StripSmallFragments.h... Generating code for file StructChecker.h... Generating code for file StructCheckerOptions.h... -Generating code for file Tautomer.h... -Generating code for file Tautomer.h... Generating code for file Utilites.h... Generating code for file Subgraphs.h... Generating code for file SubgraphUtils.h... @@ -10100,6 +10136,8 @@ Generating docs for file RegisterDescriptor.h... Generating docs for file USRDescriptor.h... Generating docs for file WHIM.h... +Generating docs for file details.h... +Generating docs for file details.h... Generating docs for file DetermineBonds.h... Generating docs for file BoundsMatrixBuilder.h... Generating docs for file Embedder.h... @@ -10148,9 +10186,7 @@ Generating docs for file SeedSet.h... Generating docs for file SubstructMatchCustom.h... Generating docs for file SubstructureCache.h... -Generating/build/reproducible-path/rdkit-202209.3/Code/GraphMol/QueryOps.h:525: warning: Found unknown command '\overloadquery' -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/QueryOps.h:534: warning: Found unknown command '\overloadquery' - docs for file Target.h... +Generating docs for file Target.h... Generating docs for file TargetMatch.h... Generating docs for file TorsionAngleM6.h... Generating docs for file TorsionPreferences.h... @@ -10212,8 +10248,6 @@ Generating docs for file mf.h... Generating docs for file MolHash.h... Generating docs for file nmmolhash.h... -Generating docs for file details.h... -Generating docs for file details.h... Generating docs for file MolInterchange.h... Generating docs for file MolOps.h... Generating docs for file MolPickler.h... @@ -10228,6 +10262,8 @@ Generating docs for file Metal.h... Generating docs for file MolStandardize.h... Generating docs for file Normalize.h... +Generating docs for file Tautomer.h... +Generating docs for file Tautomer.h... Generating docs for file TautomerCatalogEntry.h... Generating docs for file TautomerCatalogParams.h... Generating docs for file TautomerCatalogUtils.h... @@ -10242,7 +10278,9 @@ Generating docs for file GasteigerParams.h... Generating docs for file PeriodicTable.h... Generating docs for file QueryAtom.h... -Generating docs for file QueryBond.h... +Generating docs for fi/build/reproducible-path/rdkit-202209.3/Code/GraphMol/QueryOps.h:525: warning: Found unknown command '\overloadquery' +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/QueryOps.h:534: warning: Found unknown command '\overloadquery' +le QueryBond.h... Generating docs for file QueryOps.h... Generating docs for file RDKitBase.h... Generating docs for file RDKitQueries.h... @@ -10281,8 +10319,6 @@ Generating docs for file StripSmallFragments.h... Generating docs for file StructChecker.h... Generating docs for file StructCheckerOptions.h... -Generating docs for file Tautomer.h... -Generating docs for file Tautomer.h... Generating docs for file Utilites.h... Generating docs for file Subgraphs.h... Generating docs for file SubgraphUtils.h... @@ -13876,7 +13912,7 @@ /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInC++.md:1444: WARNING: None:any reference target not found: ./C++Examples/example15.cpp /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInC++.md:1472: WARNING: None:any reference target not found: ./C++Examples/example16.cpp /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInC++.md:1510: WARNING: None:any reference target not found: ./C++Examples/example16.cpp -WARNING: Could not fetch remote image: https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png%3Bbase64,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%3Bbase64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC (Caused by NewConnectionError(': Failed to establish a new connection: [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%3Bbase64,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%3Bbase64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution'))] done writing... /build/reproducible-path/rdkit-202209.3/Docs/Book/Install.md:: WARNING: Pygments lexer name 'shellsession' is not known /build/reproducible-path/rdkit-202209.3/Docs/Book/Install.md:: WARNING: Pygments lexer name 'shellsession' is not known @@ -16357,10 +16393,10 @@ /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/rdchem.so #export RDBASE=/build/reproducible-path/rdkit-202209.3 PYTHONPATH=/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu//lib:/usr/lib/libeatmydata" PYTHONPATH=/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/:/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu//rdkit/Chem/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu//lib:/usr/lib/libeatmydata" dh_auto_test - cd obj-i686-linux-gnu && make -j16 test ARGS\+=--verbose ARGS\+=-j16 + cd obj-i686-linux-gnu && make -j7 test ARGS\+=--verbose ARGS\+=-j7 make[2]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j16 +/usr/bin/ctest --force-new-ctest-process --verbose -j7 UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/DartConfiguration.tcl Add coverage exclude regular expressions. @@ -16415,62 +16451,8 @@ 7: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral/logTestsCatch 7: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral 7: Test timeout computed to be: 1500 -test 8 - Start 8: testDataStructs - -8: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/testDataStructs -8: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs -8: Test timeout computed to be: 1500 -test 9 - Start 9: testFPB - -9: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/testFPB -9: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs -9: Test timeout computed to be: 1500 -test 10 - Start 10: testMultiFPB - -10: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/testMultiFPB -10: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs -10: Test timeout computed to be: 1500 -test 11 - Start 11: pyBV - -11: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/testBV.py" -11: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap -11: Test timeout computed to be: 1500 -test 12 - Start 12: pyDiscreteValueVect - -12: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/testDiscreteValueVect.py" -12: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap -12: Test timeout computed to be: 1500 -test 13 - Start 13: pySparseIntVect - -13: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/testSparseIntVect.py" -13: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap -13: Test timeout computed to be: 1500 -test 14 - Start 14: pyFPB - -14: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/testFPB.py" -14: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap -14: Test timeout computed to be: 1500 -test 15 - Start 15: testTransforms - -15: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry/testTransforms -15: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry -15: Test timeout computed to be: 1500 -test 16 - Start 16: testGrid - -16: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry/testGrid -16: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry -16: Test timeout computed to be: 1500 -3: [19:37:05] Testing Github940: property dictionaries leaking memory -3: [19:37:05] done +3: [16:02:52] Testing Github940: property dictionaries leaking memory +3: [16:02:52] done 3: Testing RDValue 3: Testing RDAny 3: dict set int vect @@ -16487,28 +16469,49 @@ 4: == unsigned int 4: == bool 4: == std::string -5: [19:37:05] +5: [16:02:52] 5: ----------------------------------------- -5: [19:37:05] Finished: testPushAndPop() -5: [19:37:05] +5: [16:02:52] Finished: testPushAndPop() +5: [16:02:52] 5: ----------------------------------------- -5: [19:37:05] +5: [16:02:52] 5: ----------------------------------------- + 1/208 Test #4: testRDValue ............................ Passed 0.02 sec +test 8 + Start 8: testDataStructs + +8: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/testDataStructs +8: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs +8: Test timeout computed to be: 1500 6: =============================================================================== 6: All tests passed (32 assertions in 2 test cases) 6: -7: [19:37:05] should not be silent -7: [19:37:05] should not be silent -7: [19:37:05] should not be silent -7: [19:37:05] should not be silent -7: [19:37:05] should not be silent -7: [19:37:05] should not be silent -7: [19:37:05] should not be silent -7: [19:37:05] should not be silent -7: [19:37:05] should not be silent + 2/208 Test #6: dictTestsCatch ......................... Passed 0.03 sec +test 9 + Start 9: testFPB + +9: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/testFPB +9: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs +9: Test timeout computed to be: 1500 +7: [16:02:52] should not be silent +7: [16:02:52] should not be silent +7: [16:02:52] should not be silent +7: [16:02:52] should not be silent +7: [16:02:52] should not be silent +7: [16:02:52] should not be silent +7: [16:02:52] should not be silent +7: [16:02:52] should not be silent +7: [16:02:52] should not be silent 7: =============================================================================== 7: All tests passed (24 assertions in 2 test cases) 7: + 3/208 Test #7: logTestsCatch .......................... Passed 0.03 sec +test 10 + Start 10: testMultiFPB + +10: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/testMultiFPB +10: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs +10: Test timeout computed to be: 1500 8: 10, 11, 14, 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, @@ -16525,137 +16528,27 @@ 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 - 1/208 Test #4: testRDValue ............................ Passed 0.03 sec -test 17 - Start 17: geometryTestsCatch - -17: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry/geometryTestsCatch -17: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry -17: Test timeout computed to be: 1500 - 2/208 Test #6: dictTestsCatch ......................... Passed 0.03 sec -test 18 - Start 18: testPyGeometry - -18: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/testGeometry.py" -18: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry/Wrap -18: Test timeout computed to be: 1500 - 3/208 Test #7: logTestsCatch .......................... Passed 0.03 sec -test 19 - Start 19: testMatrices - -19: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/testMatrices -19: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics -19: Test timeout computed to be: 1500 - 4/208 Test #8: testDataStructs ........................ Passed 0.03 sec -test 20 - Start 20: testConrec - -20: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/testConrec -20: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics -20: Test timeout computed to be: 1500 - 5/208 Test #9: testFPB ................................ Passed 0.03 sec -test 21 - Start 21: testAlignment - -21: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment/testAlignment -21: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment -21: Test timeout computed to be: 1500 - 6/208 Test #10: testMultiFPB ........................... Passed 0.03 sec -test 22 - Start 22: pyAlignment - -22: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py" -22: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment/Wrap -22: Test timeout computed to be: 1500 -15: **************************************** -15: testPointND -15: **************************************** -15: testPointOps3D -15: **************************************** -15: testPointOps2D -15: **************************************** -15: test12D -15: ref1: 2.7929 3.07415 ref2: 4.70469 2.32958 -15: pt1: 0.545144 1.778 pt2: 2.67497 0.352085 -15: **************************************** -15: test23D -15: **************************************** -15: test3MatMultiply -15: Pt1: 1 0 0 Pt2: 2 0 0 -15: -Pt1: -1 -0 -0 -15: tp1: 0 0 0 tp2: 0 0 0 -15: tp1: 0 0 0 tp2: 0 0 0 -15: tp1: 0 0 3 tp2: 0 0 3 -15: npt1: 0 0 3 npt2: 0 0 4 -15: Pt1: 0 0 3 Pt2: 6.12323e-17 0 4 -15: **************************************** -15: testFromQuaternion -15: **************************************** - 7/208 Test #15: testTransforms ......................... Passed 0.02 sec -test 23 - Start 23: testOptimizer - -23: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Optimizer/testOptimizer -23: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Optimizer -23: Test timeout computed to be: 1500 -19: [19:37:05] ----------------------------------------- -19: [19:37:05] Testing RDNumerics: vectors and matrices Code -19: [19:37:05] --------------------------------------- -19: [19:37:05] test1Vector -19: [19:37:05] --------------------------------------- -19: [19:37:05] test2Matrix -19: [19:37:05] --------------------------------------- -19: [19:37:05] test3SquareMatrix -19: [19:37:05] --------------------------------------- -19: [19:37:05] test4SymmMatrix - 8/208 Test #19: testMatrices ........................... Passed 0.01 sec -test 24 - Start 24: testUFFForceField - -24: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/UFF/testUFFForceField -24: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/UFF -24: Test timeout computed to be: 1500 -17: =============================================================================== -17: All tests passed (50 assertions in 5 test cases) -17: - 9/208 Test #17: geometryTestsCatch ..................... Passed 0.02 sec -test 25 - Start 25: testMMFFForceField + 4/208 Test #9: testFPB ................................ Passed 0.03 sec +test 11 + Start 11: pyBV -25: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/MMFF/testMMFFForceField -25: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/MMFF -25: Test timeout computed to be: 1500 -21: ----------------------------------------- -21: Testing Alignment Code -21: --------------------------------------- -21: testBasic -21: --------------------------------------- -21: testTriangle -21: --------------------------------------- -21: testFourPts -21: --------------------------------------- -21: testReflection -21: --------------------------------------- - 10/208 Test #21: testAlignment .......................... Passed 0.01 sec -test 26 - Start 26: pyForceFieldConstraints +11: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/testBV.py" +11: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap +11: Test timeout computed to be: 1500 + 5/208 Test #8: testDataStructs ........................ Passed 0.05 sec +test 12 + Start 12: pyDiscreteValueVect -26: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/ForceField/Wrap/testConstraints.py" -26: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/Wrap -26: Test timeout computed to be: 1500 -23: ------------------------------------- -23: Testing linear search. -23: done -23: ------------------------------------- -23: Testing BFGS optimization. -23: done - 11/208 Test #23: testOptimizer .......................... Passed 0.01 sec -test 27 - Start 27: testDistGeom +12: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/testDiscreteValueVect.py" +12: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap +12: Test timeout computed to be: 1500 + 6/208 Test #10: testMultiFPB ........................... Passed 0.05 sec +test 13 + Start 13: pySparseIntVect -27: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom/testDistGeom -27: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom -27: Test timeout computed to be: 1500 +13: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/testSparseIntVect.py" +13: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap +13: Test timeout computed to be: 1500 1: core 1: RDKit 2D 1: @@ -16822,17 +16715,6 @@ 1: 10 1 1 0 1: M END 1: -20: =============================================================================== -20: test cases: 1 | 1 passed -20: assertions: - none - -20: - 12/208 Test #20: testConrec ............................. Passed 0.03 sec -test 28 - Start 28: pyDistGeom - -28: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap/rough_test.py" -28: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom/Wrap -28: Test timeout computed to be: 1500 1: core+sidechain 1: RDKit 2D 1: @@ -16871,30 +16753,6 @@ 1: 16 1 1 0 1: M END 1: -16: *********************************************************** -16: Testing Grid -16: --------------------------------- -16: testUniformGrid1 -16: -16: --------------------------------- -16: testUniformGrid2 -16: -16: --------------------------------- -16: testUniformGridPickling -16: -16: --------------------------------- -16: testGridOps -16: -16: --------------------------------- -16: testUniformGridIndexing -16: - 13/208 Test #16: testGrid ............................... Passed 0.04 sec -test 29 - Start 29: graphmolTest1 - -29: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -29: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol -29: Test timeout computed to be: 1500 1: templated 1: RDKit 2D 1: @@ -17075,360 +16933,169 @@ 1: -0.0011 -0.5713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.8659 -0.0731 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.8679 0.9269 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.7309 -0.5749 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: 2 4 1 0 -1: 4 5 1 0 -1: 5 6 1 0 -1: 5 7 1 0 -1: M END -1: -24: ------------------------------------- -24: Unit tests for force field basics. -24: done -24: ------------------------------------- -24: Unit tests for basics of UFF bond-stretch terms. -24: done -24: ------------------------------------- -24: Unit tests for UFF bond-stretch terms. -24: done -24: ------------------------------------- -24: Unit tests for basics of UFF angle terms. -24: done -24: ------------------------------------- -24: Unit tests for UFF angle-bend terms. -24: theta = 3.14159; theta0 = 3.14159 -24: theta = 2.094395, param1.theta0 = 2.094395 -24: done -24: ------------------------------------- -24: Test Simple UFF molecule optimizations. -24: done -24: ------------------------------------- -24: Unit tests for UFF nonbonded terms. -24: done -24: ------------------------------------- -24: Test UFF torsional terms. -24: done -24: ------------------------------------- -24: Test UFF Parameter objects -1: templated -1: RDKit 2D -1: -1: 7 6 0 0 0 0 0 0 0 0999 V2000 -1: 1.2184 -0.5011 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.3464 0.0006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.3450 1.0068 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.5242 -0.5035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.3910 -0.0046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.2564 -0.5056 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.3922 0.9954 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: 2 4 1 0 -1: 4 5 1 0 -1: 5 6 1 0 -1: 5 7 1 0 -1: M END -1: -1: test1 -1: RDKit 2D -1: -1: 12 12 0 0 0 0 0 0 0 0999 V2000 -1: 0.3628 0.5403 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.5014 1.0435 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.3692 0.5467 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -2.2334 1.0497 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -3.1012 0.5529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -1.3728 -0.4533 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.5086 -0.9565 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.3594 -0.4597 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1.2234 -0.9627 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.0912 -0.4657 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.0948 0.5341 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 2.9554 -0.9689 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1 2 2 0 -1: 2 3 1 0 -1: 3 4 1 0 -1: 4 5 1 0 -1: 3 6 2 0 -1: 6 7 1 0 -1: 7 8 2 0 -1: 8 9 1 0 -1: 9 10 1 0 -1: 10 11 2 0 -1: 10 12 1 0 -1: 8 1 1 0 -1: M END -1: -1: test2 -1: RDKit 2D -1: -1: 5 4 0 0 0 0 0 0 0 0999 V2000 -1: -0.4980 0.7210 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.0004 -0.1464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1: -0.8678 -0.6440 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.5020 0.7182 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 -1: 0.8642 -0.6488 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: 2 4 1 0 -1: 2 5 1 0 -1: M END -1: -24: ------------------------------------- -24: Test Simple UFF molecule optimization, part 2. -24: done -24: ------------------------------------- -24: Test UFF Torsion Conflicts. -24: C 0.4783 -0.7477 -0.0753 -24: C -0.5465 -0.0176 0.3519 -24: C -0.5114 1.4472 0.0870 -24: H -1.5201 -0.4838 0.2485 -24: H 0.4696 1.8363 0.3367 -24: O -1.2618 1.9423 0.6934 -24: F -0.7163 1.6298 -0.9622 -24: done -24: ------------------------------------- -24: Unit tests for UFF distance constraint terms. -24: done -24: ------------------------------------- -24: Unit tests for all UFF constraint terms. -27: *********************************************************** -27: test1 -27: *********************************************************** -27: testIssue216 -27: Rows: 4 Columns: 4 -27: 0 1 1 1 -27: 1 0 1 1 -27: 1 1 0 1 -27: 1 1 1 0 -27: *********************************************************** -27: -25: ------------------------------------- -25: Official MMFF validation suite. - 14/208 Test #27: testDistGeom ........................... Passed 0.02 sec -test 30 - Start 30: graphmolcpTest - -30: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/graphmolcpTest -30: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol -30: Test timeout computed to be: 1500 -29: Atoms: -29: 0 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 0 arom?: 0 chi: 0 -29: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 0 arom?: 0 chi: 0 -29: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 0 arom?: 0 chi: 0 -29: 3 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0 -29: 4 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0 -29: 5 6 C chg: 0 deg: 1 exp: 3 imp: 1 hyb: 0 arom?: 0 chi: 0 -29: 6 6 C chg: 0 deg: 2 exp: 4 imp: 0 hyb: 0 arom?: 0 chi: 0 -29: 7 7 N chg: 0 deg: 2 exp: 1 imp: 2 hyb: 0 arom?: 1 chi: 0 -29: 8 22 Ti chg: 0 deg: 1 exp: [19:37:05] -29: -29: **** -29: Pre-condition Violation -29: getExplicitValence() called without call to calcExplicitValence() -29: Violation occurred on line 306 in file ./Code/GraphMol/Atom.cpp -29: Failed Expression: d_explicitValence > -1 -29: **** -29: -29: N/A imp: -1 hyb: 0 arom?: 0 chi: 0 -29: Bonds: -29: 0 0->1 order: 1 conj?: 0 aromatic?: 0 -29: 1 1->2 order: 2 conj?: 0 aromatic?: 0 -29: 2 2->3 order: 1 conj?: 0 aromatic?: 0 -29: 3 0->4 order: 1 conj?: 0 aromatic?: 0 -29: 4 5->6 order: 3 conj?: 0 aromatic?: 0 -29: 5 6->7 order: 1 conj?: 0 aromatic?: 0 -29: 6 7->8 order: 2 conj?: 0 aromatic?: 0 -30: -30: -30: -30: COPY -29: [19:37:05] -29: -29: **** -29: Pre-condition Violation -29: bond already exists -29: Violation occurred on line 334 in file ./Code/GraphMol/RWMol.cpp -29: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) -29: **** -29: -29: [19:37:05] -29: -29: **** -29: Pre-condition Violation -29: bond already exists -29: Violation occurred on line 334 in file ./Code/GraphMol/RWMol.cpp -29: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) -29: **** -29: -29: [19:37:05] -29: -29: **** -29: Pre-condition Violation -29: attempt to add self-bond -29: Violation occurred on line 333 in file ./Code/GraphMol/RWMol.cpp -29: Failed Expression: atomIdx1 != atomIdx2 -29: **** -29: -29: [19:37:05] -29: -29: **** -29: Pre-condition Violation -29: bond already exists -29: Violation occurred on line 440 in file ./Code/GraphMol/ROMol.cpp -29: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph) .second) -29: **** -29: -29: [19:37:05] -29: -29: **** -29: Pre-condition Violation -29: attempt to add self-bond -29: Violation occurred on line 438 in file ./Code/GraphMol/ROMol.cpp -29: Failed Expression: bond_pin->getBeginAtomIdx() != bond_pin->getEndAtomIdx() -29: **** -29: -29: [19:37:05] Explicit valence for atom # 0 B, 4, is greater than permitted -29: [19:37:05] Explicit valence for atom # 0 B, 5, is greater than permitted -29: [19:37:05] -29: -29: **** -29: Post-condition Violation -29: Element 'Xx' not found -29: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -29: Failed Expression: anum > -1 -29: **** -29: -29: [19:37:05] ------------------------------------- -29: [19:37:05] Test github381: thread-safe initialization of the periodic table - 15/208 Test #30: graphmolcpTest ......................... Passed 0.03 sec -test 31 - Start 31: graphmolqueryTest - -31: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/graphmolqueryTest -31: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol -31: Test timeout computed to be: 1500 -29: [19:37:05] done -29: [19:37:05] ------------------------------------- -29: [19:37:05] Test github1041: Segfault for atom with no owner (expect some warnings) -29: [19:37:05] -29: -29: **** -29: Pre-condition Violation -29: no owner -29: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h -29: Failed Expression: dp_mol -29: **** -29: -29: [19:37:05] -29: -29: **** -29: Pre-condition Violation -29: no owner -29: Violation occurred on line 185 in file ./Code/GraphMol/Bond.h -29: Failed Expression: dp_mol -29: **** -29: -29: [19:37:05] done -29: [19:37:05] ------------------------------------- -29: [19:37:05] Test github1041: Segfault for atom with no owner (expect some warnings) -29: [19:37:05] -29: -29: **** -29: Pre-condition Violation -29: no owner -29: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h -29: Failed Expression: dp_mol -29: **** -29: -29: [19:37:05] -29: -29: **** -29: Pre-condition Violation -29: no owner -29: Violation occurred on line 185 in file ./Code/GraphMol/Bond.h -29: Failed Expression: dp_mol -29: **** -29: -29: [19:37:05] done -29: [19:37:05] ------------------------------------- -29: [19:37:05] Test github1453: RWMol.clear() should reset the numBonds count. -29: [19:37:05] done -29: [19:37:05] ------------------------------------- -29: [19:37:05] Test range-based for loops. -29: [19:37:05] done -29: [19:37:05] ------------------------------------- -29: [19:37:05] Test github1642: Atom index type is too low for big molecules. -31: [19:37:05] ---------------------- Test1 -31: [19:37:05] Done! -31: [19:37:05] ---------------------- Test2 -31: [19:37:05] Done! -31: [19:37:05] ---------------------- Test3 -31: [19:37:05] Done! -31: [19:37:05] ---------------------- Test4 -31: [19:37:05] Done! -31: [19:37:05] ---------------------- Test5 -31: [19:37:05] Done! -31: [19:37:05] Done! -31: [19:37:05] ---------------------- Test issue 2892580 -31: [19:37:05] Done! -31: [19:37:05] ---------------------- Test github issue 53: query molecules not matching [R] -31: [19:37:05] Done! -31: [19:37:05] ---------------------- Test queries using qualifiers instead of == -31: [19:37:05] Done! -31: [19:37:05] ---------------------- Test Github issue 165: radicals not used in atom-atom matching -31: [19:37:05] Done! -31: [19:37:05] ---------------------- Test extra atom queries -31: [19:37:05] Done! -31: [19:37:05] ---------------------- Test extra bond queries -31: [19:37:05] Done! -31: [19:37:05] ---------------------- Test num heteroatom neighbor queries -31: [19:37:05] Done! -31: [19:37:05] ---------------------- Test atom type queries -31: [19:37:05] Done! -31: [19:37:05] ---------------------- Test Github #2471: dummy atom queries are flagged as complex -31: [19:37:05] Done! -31: [19:37:05] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() -31: [19:37:05] Done! - 16/208 Test #31: graphmolqueryTest ...................... Passed 0.03 sec -test 32 - Start 32: graphmolMolOpsTest - -32: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/graphmolMolOpsTest -32: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol -32: Test timeout computed to be: 1500 -24: done -24: ------------------------------------- -24: Unit tests for copying UFF ForceFields. -24: done -24: ------------------------------------- -24: Unit test for UFF butane scan. -32: 1 1 2 -32: 1 1 1 -32: 2 1 0.75 -32: path: 2 -32: [19:37:05] Warning: conflicting stereochemistry at atom 10 ignored. by rule 1a. -32: [19:37:05] Warning: conflicting stereochemistry at atom 10 ignored. by rule 1a. -32: [19:37:05] Explicit valence for atom # 0 B, 5, is greater than permitted -32: [19:37:05] Explicit valence for atom # 1 C, 5, is greater than permitted -32: [19:37:05] Explicit valence for atom # 1 C, 5, is greater than permitted -32: [19:37:05] Explicit valence for atom # 1 C, 5, is greater than permitted -32: [19:37:05] Explicit valence for atom # 1 Si, 7, is greater than permitted -25: -25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... -32: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 +1: 1.7309 -0.5749 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: 2 4 1 0 +1: 4 5 1 0 +1: 5 6 1 0 +1: 5 7 1 0 +1: M END +1: +1: templated +1: RDKit 2D +1: +1: 7 6 0 0 0 0 0 0 0 0999 V2000 +1: 1.2184 -0.5011 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.3464 0.0006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.3450 1.0068 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.5242 -0.5035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.3910 -0.0046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.2564 -0.5056 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.3922 0.9954 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: 2 4 1 0 +1: 4 5 1 0 +1: 5 6 1 0 +1: 5 7 1 0 +1: M END +1: +1: test1 +1: RDKit 2D +1: +1: 12 12 0 0 0 0 0 0 0 0999 V2000 +1: 0.3628 0.5403 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.5014 1.0435 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.3692 0.5467 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -2.2334 1.0497 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -3.1012 0.5529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -1.3728 -0.4533 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.5086 -0.9565 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.3594 -0.4597 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1.2234 -0.9627 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.0912 -0.4657 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.0948 0.5341 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: 2.9554 -0.9689 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1 2 2 0 +1: 2 3 1 0 +1: 3 4 1 0 +1: 4 5 1 0 +1: 3 6 2 0 +1: 6 7 1 0 +1: 7 8 2 0 +1: 8 9 1 0 +1: 9 10 1 0 +1: 10 11 2 0 +1: 10 12 1 0 +1: 8 1 1 0 +1: M END +1: +1: test2 +1: RDKit 2D +1: +1: 5 4 0 0 0 0 0 0 0 0999 V2000 +1: -0.4980 0.7210 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.0004 -0.1464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +1: -0.8678 -0.6440 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.5020 0.7182 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 +1: 0.8642 -0.6488 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: 2 4 1 0 +1: 2 5 1 0 +1: M END +1: 12: ...... 12: ---------------------------------------------------------------------- -12: Ran 6 tests in 0.003s +12: Ran 6 tests in 0.018s 12: 12: OK 13: ......... 13: ---------------------------------------------------------------------- -13: Ran 9 tests in 0.009s +13: Ran 9 tests in 0.021s 13: 13: OK + 7/208 Test #13: pySparseIntVect ........................ Passed 0.46 sec +test 14 + Start 14: pyFPB + +14: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/testFPB.py" +14: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataStructs/Wrap +14: Test timeout computed to be: 1500 +3: static boost any:0.553251 s + 8/208 Test #12: pyDiscreteValueVect .................... Passed 0.48 sec +test 15 + Start 15: testTransforms + +15: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry/testTransforms +15: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry +15: Test timeout computed to be: 1500 +15: **************************************** +15: testPointND +15: **************************************** +15: testPointOps3D +15: **************************************** +15: testPointOps2D +15: **************************************** +15: test12D +15: ref1: 0.8887 3.55354 ref2: 0.466172 3.252 +15: pt1: 3.18879 3.15874 pt2: 3.12936 0.0381508 +15: **************************************** +15: test23D +15: **************************************** +15: test3MatMultiply +15: Pt1: 1 0 0 Pt2: 2 0 0 +15: -Pt1: -1 -0 -0 +15: tp1: 0 0 0 tp2: 0 0 0 +15: tp1: 0 0 0 tp2: 0 0 0 +15: tp1: 0 0 3 tp2: 0 0 3 +15: npt1: 0 0 3 npt2: 0 0 4 +15: Pt1: 0 0 3 Pt2: 6.12323e-17 0 4 +15: **************************************** +15: testFromQuaternion +15: **************************************** + 9/208 Test #15: testTransforms ......................... Passed 0.01 sec +test 16 + Start 16: testGrid + +16: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry/testGrid +16: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry +16: Test timeout computed to be: 1500 +16: *********************************************************** +16: Testing Grid +16: --------------------------------- +16: testUniformGrid1 +16: +16: --------------------------------- +16: testUniformGrid2 +16: +16: --------------------------------- +16: testUniformGridPickling +16: +16: --------------------------------- +16: testGridOps +16: +16: --------------------------------- +16: testUniformGridIndexing +16: + 10/208 Test #16: testGrid ............................... Passed 0.05 sec +test 17 + Start 17: geometryTestsCatch + +17: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry/geometryTestsCatch +17: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry +17: Test timeout computed to be: 1500 +17: =============================================================================== +17: All tests passed (50 assertions in 5 test cases) +17: + 11/208 Test #17: geometryTestsCatch ..................... Passed 0.02 sec +test 18 + Start 18: testPyGeometry + +18: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/testGeometry.py" +18: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Geometry/Wrap +18: Test timeout computed to be: 1500 1: cyclosporine a 1: RDKit 2D 1: @@ -17697,6 +17364,163 @@ 1: 10 2 1 0 1: M END 1: +2: .... +2: ---------------------------------------------------------------------- +2: Ran 4 tests in 0.078s +2: +2: OK + 12/208 Test #2: pyCoordGen ............................. Passed 0.70 sec +test 19 + Start 19: testMatrices + +19: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/testMatrices +19: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics +19: Test timeout computed to be: 1500 +19: [16:02:52] ----------------------------------------- +19: [16:02:52] Testing RDNumerics: vectors and matrices Code +19: [16:02:52] --------------------------------------- +19: [16:02:52] test1Vector +19: [16:02:52] --------------------------------------- +19: [16:02:52] test2Matrix +19: [16:02:52] --------------------------------------- +19: [16:02:52] test3SquareMatrix +19: [16:02:52] --------------------------------------- +19: [16:02:52] test4SymmMatrix + 13/208 Test #19: testMatrices ........................... Passed 0.01 sec +test 20 + Start 20: testConrec + +20: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/testConrec +20: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics +20: Test timeout computed to be: 1500 + 14/208 Test #1: testCoordGen ........................... Passed 0.72 sec +test 21 + Start 21: testAlignment + +21: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment/testAlignment +21: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment +21: Test timeout computed to be: 1500 +21: ----------------------------------------- +21: Testing Alignment Code +21: --------------------------------------- +21: testBasic +21: --------------------------------------- +21: testTriangle +21: --------------------------------------- +21: testFourPts +21: --------------------------------------- +21: testReflection +21: --------------------------------------- + 15/208 Test #21: testAlignment .......................... Passed 0.01 sec +test 22 + Start 22: pyAlignment + +22: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py" +22: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Alignment/Wrap +22: Test timeout computed to be: 1500 +20: =============================================================================== +20: test cases: 1 | 1 passed +20: assertions: - none - +20: + 16/208 Test #20: testConrec ............................. Passed 0.02 sec +test 23 + Start 23: testOptimizer + +23: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Optimizer/testOptimizer +23: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics/Optimizer +23: Test timeout computed to be: 1500 +23: ------------------------------------- +23: Testing linear search. +23: done +23: ------------------------------------- +23: Testing BFGS optimization. +23: done + 17/208 Test #23: testOptimizer .......................... Passed 0.01 sec +test 24 + Start 24: testUFFForceField + +24: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/UFF/testUFFForceField +24: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/UFF +24: Test timeout computed to be: 1500 +24: ------------------------------------- +24: Unit tests for force field basics. +24: done +24: ------------------------------------- +24: Unit tests for basics of UFF bond-stretch terms. +24: done +24: ------------------------------------- +24: Unit tests for UFF bond-stretch terms. +24: done +24: ------------------------------------- +24: Unit tests for basics of UFF angle terms. +24: done +24: ------------------------------------- +24: Unit tests for UFF angle-bend terms. +24: theta = 3.14159; theta0 = 3.14159 +24: theta = 2.094395, param1.theta0 = 2.094395 +24: done +24: ------------------------------------- +24: Test Simple UFF molecule optimizations. +24: done +24: ------------------------------------- +24: Unit tests for UFF nonbonded terms. +24: done +24: ------------------------------------- +24: Test UFF torsional terms. +24: done +24: ------------------------------------- +24: Test UFF Parameter objects +24: ------------------------------------- +24: Test Simple UFF molecule optimization, part 2. +24: done +24: ------------------------------------- +24: Test UFF Torsion Conflicts. +24: C 0.4783 -0.7477 -0.0753 +24: C -0.5465 -0.0176 0.3519 +24: C -0.5114 1.4472 0.0870 +24: H -1.5201 -0.4838 0.2485 +24: H 0.4696 1.8363 0.3367 +24: O -1.2618 1.9423 0.6934 +24: F -0.7163 1.6298 -0.9622 +24: done +24: ------------------------------------- +24: Unit tests for UFF distance constraint terms. +24: done +24: ------------------------------------- +24: Unit tests for all UFF constraint terms. +14: ......... +14: ---------------------------------------------------------------------- +14: Ran 9 tests in 0.018s +14: +14: OK + 18/208 Test #14: pyFPB .................................. Passed 0.24 sec +test 25 + Start 25: testMMFFForceField + +25: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/MMFF/testMMFFForceField +25: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/MMFF +25: Test timeout computed to be: 1500 +25: ------------------------------------- +25: Official MMFF validation suite. +24: done +24: ------------------------------------- +24: Unit tests for copying UFF ForceFields. +24: done +24: ------------------------------------- +24: Unit test for UFF butane scan. +18: ........... +18: ---------------------------------------------------------------------- +18: Ran 11 tests in 0.051s +18: +18: OK +18: Testing Geometry wrapper + 19/208 Test #18: testPyGeometry ......................... Passed 0.31 sec +test 26 + Start 26: pyForceFieldConstraints + +26: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/ForceField/Wrap/testConstraints.py" +26: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ForceField/Wrap +26: Test timeout computed to be: 1500 22: EEE.. 22: ====================================================================== 22: ERROR: test1Basic (__main__.TestCase.test1Basic) @@ -17745,7 +17569,82 @@ 22: 22: FAILED (errors=3) 22: Testing Alignment Wrapper code: -32: [19:37:05] non-ring atom 0 marked aromatic +25: +25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... + 20/208 Test #22: pyAlignment ............................***Failed 0.26 sec +EEE.. +====================================================================== +ERROR: test1Basic (__main__.TestCase.test1Basic) +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py", line 41, in test1Basic + refPts = np.zeros((2, 3), np.float) + ^^^^^^^^ + File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ + raise AttributeError(__former_attrs__[attr]) +AttributeError: module 'numpy' has no attribute 'float'. +`np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here. +The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: + https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations + +====================================================================== +ERROR: test2Weights (__main__.TestCase.test2Weights) +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py", line 79, in test2Weights + np.float) + ^^^^^^^^ + File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ + raise AttributeError(__former_attrs__[attr]) +AttributeError: module 'numpy' has no attribute 'float'. +`np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here. +The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: + https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations + +====================================================================== +ERROR: test3tetra (__main__.TestCase.test3tetra) +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py", line 109, in test3tetra + np.float) + ^^^^^^^^ + File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ + raise AttributeError(__former_attrs__[attr]) +AttributeError: module 'numpy' has no attribute 'float'. +`np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here. +The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: + https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations + +---------------------------------------------------------------------- +Ran 5 tests in 0.003s + +FAILED (errors=3) +Testing Alignment Wrapper code: + +test 27 + Start 27: testDistGeom + +27: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom/testDistGeom +27: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom +27: Test timeout computed to be: 1500 +27: *********************************************************** +27: test1 +27: *********************************************************** +27: testIssue216 +27: Rows: 4 Columns: 4 +27: 0 1 1 1 +27: 1 0 1 1 +27: 1 1 0 1 +27: 1 1 1 0 +27: *********************************************************** +27: + 21/208 Test #27: testDistGeom ........................... Passed 0.02 sec +test 28 + Start 28: pyDistGeom + +28: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap/rough_test.py" +28: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DistGeom/Wrap +28: Test timeout computed to be: 1500 28: EEEEEE 28: ====================================================================== 28: ERROR: test1SmoothPass (__main__.TestCase.test1SmoothPass) @@ -17763,7 +17662,6 @@ 28: 28: ====================================================================== 28: ERROR: test2SmoothFail (__main__.TestCase.test2SmoothFail) -32: [19:37:05] non-ring atom 0 marked aromatic 28: ---------------------------------------------------------------------- 28: Traceback (most recent call last): 28: File "/build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap/rough_test.py", line 37, in test2SmoothFail @@ -17836,100 +17734,7 @@ 28: Ran 6 tests in 0.003s 28: 28: FAILED (errors=6) -14: ......... -14: ---------------------------------------------------------------------- -14: Ran 9 tests in 0.006s -14: -14: OK - 17/208 Test #12: pyDiscreteValueVect .................... Passed 0.29 sec -test 33 - Start 33: graphmoltestChirality - -33: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/graphmoltestChirality -33: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol -33: Test timeout computed to be: 1500 - 18/208 Test #13: pySparseIntVect ........................ Passed 0.29 sec -test 34 - Start 34: graphmoltestPickler - -34: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/graphmoltestPickler -34: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol -34: Test timeout computed to be: 1500 -32: [19:37:05] Conflicting single bond directions around double bond at index 17. -32: [19:37:05] BondStereo set to STEREONONE and single bond directions set to NONE. -32: starting ring finding -32: done -32: starting ring finding -32: done -32: starting ring finding -32: done -32: 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 -32: starting sanitization - 19/208 Test #22: pyAlignment ............................***Failed 0.29 sec -EEE.. -====================================================================== -ERROR: test1Basic (__main__.TestCase.test1Basic) ----------------------------------------------------------------------- -Traceback (most recent call last): - File "/build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py", line 41, in test1Basic - refPts = np.zeros((2, 3), np.float) - ^^^^^^^^ - File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ - raise AttributeError(__former_attrs__[attr]) -AttributeError: module 'numpy' has no attribute 'float'. -`np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here. -The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: - https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations - -====================================================================== -ERROR: test2Weights (__main__.TestCase.test2Weights) ----------------------------------------------------------------------- -Traceback (most recent call last): - File "/build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py", line 79, in test2Weights - np.float) - ^^^^^^^^ - File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ - raise AttributeError(__former_attrs__[attr]) -AttributeError: module 'numpy' has no attribute 'float'. -`np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here. -The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: - https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations - -====================================================================== -ERROR: test3tetra (__main__.TestCase.test3tetra) ----------------------------------------------------------------------- -Traceback (most recent call last): - File "/build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py", line 109, in test3tetra - np.float) - ^^^^^^^^ - File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ - raise AttributeError(__former_attrs__[attr]) -AttributeError: module 'numpy' has no attribute 'float'. -`np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here. -The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: - https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations - ----------------------------------------------------------------------- -Ran 5 tests in 0.003s - -FAILED (errors=3) -Testing Alignment Wrapper code: - -test 35 - Start 35: graphmoltestPicklerGlobalSetting - -35: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting -35: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol -35: Test timeout computed to be: 1500 -34: [19:37:05] ------------------------------------- -34: [19:37:05] Testing String Pickle Roundtrips. -18: ........... -18: ---------------------------------------------------------------------- -18: Ran 11 tests in 0.046s -18: -18: OK -18: Testing Geometry wrapper - 20/208 Test #28: pyDistGeom .............................***Failed 0.27 sec + 22/208 Test #28: pyDistGeom .............................***Failed 0.22 sec EEEEEE ====================================================================== ERROR: test1SmoothPass (__main__.TestCase.test1SmoothPass) @@ -18020,27 +17825,241 @@ FAILED (errors=6) -test 36 - Start 36: graphmolIterTest +test 29 + Start 29: graphmolTest1 -36: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/graphmolIterTest -36: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol -36: Test timeout computed to be: 1500 -32: done - 21/208 Test #1: testCoordGen ........................... Passed 0.34 sec -test 37 - Start 37: hanoiTest +29: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +29: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol +29: Test timeout computed to be: 1500 +29: Atoms: +29: 0 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 0 arom?: 0 chi: 0 +29: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 0 arom?: 0 chi: 0 +29: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 0 arom?: 0 chi: 0 +29: 3 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0 +29: 4 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0 +29: 5 6 C chg: 0 deg: 1 exp: 3 imp: 1 hyb: 0 arom?: 0 chi: 0 +29: 6 6 C chg: 0 deg: 2 exp: 4 imp: 0 hyb: 0 arom?: 0 chi: 0 +29: 7 7 N chg: 0 deg: 2 exp: 1 imp: 2 hyb: 0 arom?: 1 chi: 0 +29: 8 22 Ti chg: 0 deg: 1 exp: [16:02:53] +29: +29: **** +29: Pre-condition Violation +29: getExplicitValence() called without call to calcExplicitValence() +29: Violation occurred on line 306 in file ./Code/GraphMol/Atom.cpp +29: Failed Expression: d_explicitValence > -1 +29: **** +29: +29: N/A imp: -1 hyb: 0 arom?: 0 chi: 0 +29: Bonds: +29: 0 0->1 order: 1 conj?: 0 aromatic?: 0 +29: 1 1->2 order: 2 conj?: 0 aromatic?: 0 +29: 2 2->3 order: 1 conj?: 0 aromatic?: 0 +29: 3 0->4 order: 1 conj?: 0 aromatic?: 0 +29: 4 5->6 order: 3 conj?: 0 aromatic?: 0 +29: 5 6->7 order: 1 conj?: 0 aromatic?: 0 +29: 6 7->8 order: 2 conj?: 0 aromatic?: 0 +29: [16:02:53] +29: +29: **** +29: Pre-condition Violation +29: bond already exists +29: Violation occurred on line 334 in file ./Code/GraphMol/RWMol.cpp +29: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) +29: **** +29: +29: [16:02:53] +29: +29: **** +29: Pre-condition Violation +29: bond already exists +29: Violation occurred on line 334 in file ./Code/GraphMol/RWMol.cpp +29: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) +29: **** +29: +29: [16:02:53] +29: +29: **** +29: Pre-condition Violation +29: attempt to add self-bond +29: Violation occurred on line 333 in file ./Code/GraphMol/RWMol.cpp +29: Failed Expression: atomIdx1 != atomIdx2 +29: **** +29: +29: [16:02:53] +29: +29: **** +29: Pre-condition Violation +29: bond already exists +29: Violation occurred on line 440 in file ./Code/GraphMol/ROMol.cpp +29: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph) .second) +29: **** +29: +29: [16:02:53] +29: +29: **** +29: Pre-condition Violation +29: attempt to add self-bond +29: Violation occurred on line 438 in file ./Code/GraphMol/ROMol.cpp +29: Failed Expression: bond_pin->getBeginAtomIdx() != bond_pin->getEndAtomIdx() +29: **** +29: +29: [16:02:53] Explicit valence for atom # 0 B, 4, is greater than permitted +29: [16:02:53] Explicit valence for atom # 0 B, 5, is greater than permitted +24: done + 23/208 Test #24: testUFFForceField ...................... Passed 0.52 sec +test 30 + Start 30: graphmolcpTest -37: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/hanoiTest -37: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol -37: Test timeout computed to be: 1500 - 22/208 Test #14: pyFPB .................................. Passed 0.32 sec -test 38 - Start 38: graphmolMemTest1 +30: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/graphmolcpTest +30: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol +30: Test timeout computed to be: 1500 +29: [16:02:53] +29: +29: **** +29: Post-condition Violation +29: Element 'Xx' not found +29: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +29: Failed Expression: anum > -1 +29: **** +29: +29: [16:02:53] ------------------------------------- +29: [16:02:53] Test github381: thread-safe initialization of the periodic table +29: [16:02:53] done +29: [16:02:53] ------------------------------------- +29: [16:02:53] Test github1041: Segfault for atom with no owner (expect some warnings) +29: [16:02:53] +29: +29: **** +29: Pre-condition Violation +29: no owner +29: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h +29: Failed Expression: dp_mol +29: **** +29: +29: [16:02:53] +29: +29: **** +29: Pre-condition Violation +29: no owner +29: Violation occurred on line 185 in file ./Code/GraphMol/Bond.h +29: Failed Expression: dp_mol +29: **** +29: +29: [16:02:53] done +29: [16:02:53] ------------------------------------- +29: [16:02:53] Test github1041: Segfault for atom with no owner (expect some warnings) +29: [16:02:53] +29: +29: **** +29: Pre-condition Violation +29: no owner +29: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h +29: Failed Expression: dp_mol +29: **** +29: +29: [16:02:53] +29: +29: **** +29: Pre-condition Violation +29: no owner +29: Violation occurred on line 185 in file ./Code/GraphMol/Bond.h +29: Failed Expression: dp_mol +29: **** +29: +29: [16:02:53] done +29: [16:02:53] ------------------------------------- +29: [16:02:53] Test github1453: RWMol.clear() should reset the numBonds count. +29: [16:02:53] done +29: [16:02:53] ------------------------------------- +29: [16:02:53] Test range-based for loops. +29: [16:02:53] done +29: [16:02:53] ------------------------------------- +29: [16:02:53] Test github1642: Atom index type is too low for big molecules. +30: +30: +30: +30: COPY + 24/208 Test #30: graphmolcpTest ......................... Passed 0.03 sec +test 31 + Start 31: graphmolqueryTest -38: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/graphmolMemTest1 -38: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol -38: Test timeout computed to be: 1500 +31: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/graphmolqueryTest +31: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol +31: Test timeout computed to be: 1500 +31: [16:02:53] ---------------------- Test1 +31: [16:02:53] Done! +31: [16:02:53] ---------------------- Test2 +31: [16:02:53] Done! +31: [16:02:53] ---------------------- Test3 +31: [16:02:53] Done! +31: [16:02:53] ---------------------- Test4 +31: [16:02:53] Done! +31: [16:02:53] ---------------------- Test5 +31: [16:02:53] Done! +31: [16:02:53] Done! +31: [16:02:53] ---------------------- Test issue 2892580 +31: [16:02:53] Done! +31: [16:02:53] ---------------------- Test github issue 53: query molecules not matching [R] +31: [16:02:53] Done! +31: [16:02:53] ---------------------- Test queries using qualifiers instead of == +31: [16:02:53] Done! +31: [16:02:53] ---------------------- Test Github issue 165: radicals not used in atom-atom matching +31: [16:02:53] Done! +31: [16:02:53] ---------------------- Test extra atom queries +31: [16:02:53] Done! +31: [16:02:53] ---------------------- Test extra bond queries +31: [16:02:53] Done! +31: [16:02:53] ---------------------- Test num heteroatom neighbor queries +31: [16:02:53] Done! +31: [16:02:53] ---------------------- Test atom type queries +31: [16:02:53] Done! +31: [16:02:53] ---------------------- Test Github #2471: dummy atom queries are flagged as complex +31: [16:02:53] Done! +31: [16:02:53] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() +31: [16:02:53] Done! + 25/208 Test #31: graphmolqueryTest ...................... Passed 0.03 sec +test 32 + Start 32: graphmolMolOpsTest + +32: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/graphmolMolOpsTest +32: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol +32: Test timeout computed to be: 1500 +32: 1 1 2 +32: 1 1 1 +32: 2 1 0.75 +32: path: 2 +32: [16:02:53] Warning: conflicting stereochemistry at atom 10 ignored. by rule 1a. +32: [16:02:53] Warning: conflicting stereochemistry at atom 10 ignored. by rule 1a. +32: [16:02:53] Explicit valence for atom # 0 B, 5, is greater than permitted +32: [16:02:53] Explicit valence for atom # 1 C, 5, is greater than permitted +32: [16:02:53] Explicit valence for atom # 1 C, 5, is greater than permitted +32: [16:02:53] Explicit valence for atom # 1 C, 5, is greater than permitted +32: [16:02:53] Explicit valence for atom # 1 Si, 7, is greater than permitted +26: ...[16:02:53] Warning: molecule is tagged as 3D, but all Z coords are zero +26: [16:02:53] Molecule does not have explicit Hs. Consider calling AddHs() +26: [16:02:53] +26: +26: **** +26: Invariant Violation +26: bad direction in linearSearch +26: Violation occurred on line 240 in file ./Code/Numerics/Optimizer/BFGSOpt.h +26: Failed Expression: status >= 0 +26: **** +26: +32: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 +32: [16:02:53] non-ring atom 0 marked aromatic +32: [16:02:53] non-ring atom 0 marked aromatic +32: [16:02:53] Conflicting single bond directions around double bond at index 17. +32: [16:02:53] BondStereo set to STEREONONE and single bond directions set to NONE. +32: starting ring finding +32: done +32: starting ring finding +32: done +32: starting ring finding +32: done +32: 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 +32: starting sanitization +32: done 32: starting sanitization 32: done 32: starting ring finding @@ -18048,153 +18067,70 @@ 32: starting ring finding 32: done 32: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 -35: [19:37:05] done - 23/208 Test #35: graphmoltestPicklerGlobalSetting ....... Passed 0.02 sec -test 39 - Start 39: resMolSupplierTest +32: [16:02:53] WARNING: not removing hydrogen atom with dummy atom neighbors +32: ------------------------------- +32: [16:02:53] Explicit valence for atom # 0 N, 4, is greater than permitted +32: [16:02:53] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +32: [16:02:53] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +32: [16:02:53] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +32: [16:02:53] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +32: [16:02:53] WARNING: not removing hydrogen atom with dummy atom neighbors +26: ......[16:02:53] Warning: molecule is tagged as 3D, but all Z coords are zero +26: [16:02:53] Molecule does not have explicit Hs. Consider calling AddHs() +26: [16:02:53] +26: +26: **** +26: Invariant Violation +26: bad direction in linearSearch +26: Violation occurred on line 240 in file ./Code/Numerics/Optimizer/BFGSOpt.h +26: Failed Expression: status >= 0 +26: **** +26: +3: dynamic boost any:1.23872 s +3: static RDAny:0.075132 s +26: ... +26: ---------------------------------------------------------------------- +26: Ran 12 tests in 0.684s +26: +26: OK + 26/208 Test #26: pyForceFieldConstraints ................ Passed 1.02 sec +test 33 + Start 33: graphmoltestChirality -39: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/resMolSupplierTest -39: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol -39: Test timeout computed to be: 1500 +33: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/graphmoltestChirality +33: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol +33: Test timeout computed to be: 1500 +32: [16:02:54] Maximum BFS search size exceeded. +32: This is likely due to a highly symmetric fused ring system. 33: -------------------------- 33: -------------------------- 33: C/C=C/C(C)Cl - 24/208 Test #38: graphmolMemTest1 ....................... Passed 0.01 sec -test 40 - Start 40: molBundleTest - -40: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/molBundleTest -40: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol -40: Test timeout computed to be: 1500 - 25/208 Test #18: testPyGeometry ......................... Passed 0.33 sec -test 41 - Start 41: testSGroup - -41: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/testSGroup -41: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol -41: Test timeout computed to be: 1500 -32: [19:37:05] WARNING: not removing hydrogen atom with dummy atom neighbors - 26/208 Test #36: graphmolIterTest ....................... Passed 0.03 sec -test 42 - Start 42: test-valgrind - -42: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/test-valgrind -42: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol -42: Test timeout computed to be: 1500 -32: ------------------------------- -32: [19:37:05] Explicit valence for atom # 0 N, 4, is greater than permitted -32: [19:37:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -32: [19:37:05] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -32: [19:37:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -32: [19:37:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -24: done - 27/208 Test #24: testUFFForceField ...................... Passed 0.33 sec -test 43 - Start 43: graphmolTestsCatch - -43: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -43: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol -43: Test timeout computed to be: 1500 - 28/208 Test #40: molBundleTest .......................... Passed 0.03 sec -test 44 - Start 44: graphmolSGroupCatch - -44: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/graphmolSGroupCatch -44: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol -44: Test timeout computed to be: 1500 - 29/208 Test #42: test-valgrind .......................... Passed 0.02 sec -test 45 - Start 45: graphmolAdjustQueryCatch - -45: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch -45: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol -45: Test timeout computed to be: 1500 -33: [19:37:05] Conflicting single bond directions around double bond at index 2. -33: [19:37:05] BondStereo set to STEREONONE and single bond directions set to NONE. -33: [19:37:05] Conflicting single bond directions around double bond at index 4. -33: [19:37:05] BondStereo set to STEREONONE and single bond directions set to NONE. -33: [19:37:05] Conflicting single bond directions around double bond at index 15. -33: [19:37:05] BondStereo set to STEREONONE and single bond directions set to NONE. -33: [19:37:05] Conflicting single bond directions around double bond at index 2. -33: [19:37:05] BondStereo set to STEREONONE and single bond directions set to NONE. -33: [19:37:05] Conflicting single bond directions around double bond at index 1. -33: [19:37:05] BondStereo set to STEREONONE and single bond directions set to NONE. -32: [19:37:05] WARNING: not removing hydrogen atom with dummy atom neighbors -34: [19:37:05] done -34: [19:37:05] ------------------------------------- -34: [19:37:05] Testing reading existing pickle file (v2). -2: .... -2: ---------------------------------------------------------------------- -2: Ran 4 tests in 0.048s -2: -2: OK - 30/208 Test #41: testSGroup ............................. Passed 0.04 sec -test 46 - Start 46: chiralityTestsCatch - -46: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/chiralityTestsCatch -46: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol -46: Test timeout computed to be: 1500 +33: [16:02:54] Conflicting single bond directions around double bond at index 2. +33: [16:02:54] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [16:02:54] Conflicting single bond directions around double bond at index 4. +33: [16:02:54] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [16:02:54] Conflicting single bond directions around double bond at index 15. +33: [16:02:54] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [16:02:54] Conflicting single bond directions around double bond at index 2. +33: [16:02:54] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [16:02:54] Conflicting single bond directions around double bond at index 1. +33: [16:02:54] BondStereo set to STEREONONE and single bond directions set to NONE. 33: -------------------------------------------------- - 31/208 Test #33: graphmoltestChirality .................. Passed 0.10 sec -test 47 - Start 47: canonTestsCatch - -47: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/canonTestsCatch -47: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol -47: Test timeout computed to be: 1500 -43: [19:37:05] WARNING: not removing hydrogen atom without neighbors -43: [19:37:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [19:37:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [19:37:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -44: =============================================================================== -44: All tests passed (120 assertions in 6 test cases) -44: -43: [19:37:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. - 32/208 Test #44: graphmolSGroupCatch .................... Passed 0.04 sec -test 48 - Start 48: moliteratorTestsCatch - -48: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/moliteratorTestsCatch -48: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol -48: Test timeout computed to be: 1500 -43: [19:37:05] Explicit valence for atom # 1 N, 5, is greater than permitted -43: [19:37:05] Explicit valence for atom # 1 N, 6, is greater than permitted -43: [19:37:05] Explicit valence for atom # 1 N, 5, is greater than permitted -43: [19:37:05] Explicit valence for atom # 1 N, 5, is greater than permitted -43: [19:37:05] Explicit valence for atom # 2 O, 3, is greater than permitted -43: [19:37:05] Explicit valence for atom # 2 O, 3, is greater than permitted -43: [19:37:05] non-ring atom 2 marked aromatic -43: [19:37:05] non-ring atom 2 marked aromatic -43: [19:37:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [19:37:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [19:37:05] Can't kekulize mol. Unkekulized atoms: 1 2 3 -43: [19:37:05] Can't kekulize mol. Unkekulized atoms: 1 2 3 -43: [19:37:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 -43: [19:37:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 -43: [19:37:05] Explicit valence for atom # 1 O, 3, is greater than permitted -43: [19:37:05] Explicit valence for atom # 4 F, 2, is greater than permitted -43: [19:37:05] Can't kekulize mol. Unkekulized atoms: 6 7 8 -43: [19:37:05] Explicit valence for atom # 1 C, 5, is greater than permitted -43: [19:37:05] WARNING: not removing hydrogen atom with dummy atom neighbors -43: [19:37:05] WARNING: not removing hydrogen atom with dummy atom neighbors -43: [19:37:05] WARNING: not removing hydrogen atom with wedged bond -43: [19:37:05] WARNING: not removing hydrogen atom without neighbors -43: [19:37:05] WARNING: not removing hydrogen atom without neighbors -3: static boost any:0.420147 s - 33/208 Test #2: pyCoordGen ............................. Passed 0.43 sec -test 49 - Start 49: testDepictor + 27/208 Test #33: graphmoltestChirality .................. Passed 0.10 sec +test 34 + Start 34: graphmoltestPickler -49: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/testDepictor -49: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor -49: Test timeout computed to be: 1500 -43: [19:37:05] WARNING: not removing hydrogen atom without neighbors -43: [19:37:05] WARNING: not removing hydrogen atom without neighbors -43: [19:37:05] Unreasonable formal charge on hydrogen # 0. -34: [19:37:05] done -34: [19:37:05] ------------------------------------- -34: [19:37:05] Testing combining molecules using pickles. +34: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/graphmoltestPickler +34: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol +34: Test timeout computed to be: 1500 +34: [16:02:54] ------------------------------------- +34: [16:02:54] Testing String Pickle Roundtrips. +34: [16:02:54] done +34: [16:02:54] ------------------------------------- +34: [16:02:54] Testing reading existing pickle file (v2). +34: [16:02:54] done +34: [16:02:54] ------------------------------------- +34: [16:02:54] Testing combining molecules using pickles. 34: Atoms: 34: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 34: 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 @@ -18211,205 +18147,37 @@ 34: 4 4->5 order: 1 conj?: 0 aromatic?: 0 34: 5 5->6 order: 1 conj?: 0 aromatic?: 0 34: 6 6->3 order: 1 conj?: 0 aromatic?: 0 -34: [19:37:05] done -34: [19:37:05] ------------------------------------- -34: [19:37:05] Testing Issue164: Roundtrip Pickle Failure. -43: [19:37:05] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() -43: [19:37:05] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() -43: [19:37:05] -43: -43: **** -43: Pre-condition Violation -43: no atom -43: Violation occurred on line 183 in file ./Code/GraphMol/ROMol.cpp -43: Failed Expression: at -43: **** -43: -43: [19:37:05] -43: -43: **** -43: Pre-condition Violation -43: atom not associated with a molecule -43: Violation occurred on line 184 in file ./Code/GraphMol/ROMol.cpp -43: Failed Expression: at->hasOwningMol() -43: **** -43: -43: [19:37:05] -43: -43: **** -43: Pre-condition Violation -43: atom not associated with this molecule -43: Violation occurred on line 185 in file ./Code/GraphMol/ROMol.cpp -43: Failed Expression: &at->getOwningMol() == this -43: **** -43: -43: [19:37:05] -43: -43: **** -43: Pre-condition Violation -43: no atom -43: Violation occurred on line 382 in file ./Code/GraphMol/ROMol.cpp -43: Failed Expression: at -43: **** -43: -43: [19:37:05] -43: -43: **** -43: Pre-condition Violation -43: atom not associated with a molecule -43: Violation occurred on line 383 in file ./Code/GraphMol/ROMol.cpp -43: Failed Expression: at->hasOwningMol() -43: **** -43: -43: [19:37:05] -43: -43: **** -43: Pre-condition Violation -43: atom not associated with this molecule -43: Violation occurred on line 384 in file ./Code/GraphMol/ROMol.cpp -43: Failed Expression: &at->getOwningMol() == this -43: **** -43: -43: [19:37:05] -43: -43: **** -43: Pre-condition Violation -43: no atom -43: Violation occurred on line 390 in file ./Code/GraphMol/ROMol.cpp -43: Failed Expression: at -43: **** -43: -43: [19:37:05] -43: -43: **** -43: Pre-condition Violation -43: atom not associated with a molecule -43: Violation occurred on line 391 in file ./Code/GraphMol/ROMol.cpp -43: Failed Expression: at->hasOwningMol() -43: **** -43: -43: [19:37:05] -43: -43: **** -43: Pre-condition Violation -43: atom not associated with this molecule -43: Violation occurred on line 392 in file ./Code/GraphMol/ROMol.cpp -43: Failed Expression: &at->getOwningMol() == this -43: **** -43: -43: [19:37:05] -43: -43: **** -43: Pre-condition Violation -43: null atom passed in -43: Violation occurred on line 406 in file ./Code/GraphMol/ROMol.cpp -43: Failed Expression: atom_pin -43: **** -43: -43: [19:37:05] -43: -43: **** -43: Pre-condition Violation -43: cannot take ownership of an atom which already has an owner -43: Violation occurred on line 407 in file ./Code/GraphMol/ROMol.cpp -43: Failed Expression: !takeOwnership || !atom_pin->hasOwningMol() || &atom_pin->getOwningMol() == this -43: **** -43: -43: [19:37:05] -43: -43: **** -43: Pre-condition Violation -43: cannot take ownership of an bond which already has an owner -43: Violation occurred on line 433 in file ./Code/GraphMol/ROMol.cpp -43: Failed Expression: !takeOwnership || !bond_pin->hasOwningMol() || &bond_pin->getOwningMol() == this -43: **** -43: -43: [19:37:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [19:37:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -34: [19:37:05] done -34: [19:37:05] ------------------------------------- -34: [19:37:05] Testing Issue219: Pickle Failure with Conformations. -43: [19:37:05] WARNING: not removing hydrogen atom without neighbors -43: [19:37:05] Explicit valence for atom # 1 F greater than permitted -34: [19:37:05] done -34: [19:37:05] ------------------------------------- -34: [19:37:05] Testing Issue220: Pickle problems with bond stereochemistry. -43: [19:37:05] -43: -43: **** -43: Pre-condition Violation -43: plain atoms have no Query -43: Violation occurred on line 625 in file ./Code/GraphMol/Atom.cpp -43: Failed Expression: 0 -43: **** -43: -43: [19:37:05] -43: -43: **** -43: Pre-condition Violation -43: plain atoms have no Query -43: Violation occurred on line 630 in file ./Code/GraphMol/Atom.cpp -43: Failed Expression: 0 -43: **** -43: -34: [19:37:05] done -34: [19:37:05] ------------------------------------- -34: [19:37:05] Testing query serialization. -43: [19:37:05] -43: -43: **** -43: Pre-condition Violation -43: plain bonds have no Query -43: Violation occurred on line 206 in file ./Code/GraphMol/Bond.cpp -43: Failed Expression: 0 -43: **** -43: -43: [19:37:05] -43: -43: **** -43: Pre-condition Violation -43: plain bonds have no query -43: Violation occurred on line 227 in file ./Code/GraphMol/Bond.cpp -43: Failed Expression: 0 -43: **** -43: -47: 2 6 8 4 9 0 7 3 5 1 -47: 1 5 7 3 9 0 8 4 6 2 -47: 1 5 7 3 9 0 8 4 6 2 -47: 1 5 7 3 9 0 8 4 6 2 -47: =============================================================================== -47: All tests passed (47 assertions in 2 test cases) -47: -43: [19:37:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [19:37:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [19:37:05] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -43: [19:37:05] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -34: [19:37:05] C=[$(C=O)] -34: [19:37:05] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] - 34/208 Test #47: canonTestsCatch ........................ Passed 0.03 sec -test 50 - Start 50: depictorCatch - -50: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/depictorCatch -50: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor -50: Test timeout computed to be: 1500 -34: [19:37:05] done -34: [19:37:05] ------------------------------------- -34: [19:37:05] Testing radical handling in pickles. -34: [19:37:05] done -34: [19:37:05] done -34: [19:37:05] ------------------------------------- -34: [19:37:05] Testing sf.net issue 2788233. -34: [19:37:05] done -34: [19:37:05] ------------------------------------- -34: [19:37:05] Testing sf.net issue 3202580. +34: [16:02:54] done +34: [16:02:54] ------------------------------------- +34: [16:02:54] Testing Issue164: Roundtrip Pickle Failure. +34: [16:02:54] done +34: [16:02:54] ------------------------------------- +34: [16:02:54] Testing Issue219: Pickle Failure with Conformations. +34: [16:02:54] done +34: [16:02:54] ------------------------------------- +34: [16:02:54] Testing Issue220: Pickle problems with bond stereochemistry. +34: [16:02:54] done +34: [16:02:54] ------------------------------------- +34: [16:02:54] Testing query serialization. +34: [16:02:54] C=[$(C=O)] +34: [16:02:54] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] +34: [16:02:54] done +34: [16:02:54] ------------------------------------- +34: [16:02:54] Testing radical handling in pickles. +34: [16:02:54] done +34: [16:02:54] done +34: [16:02:54] ------------------------------------- +34: [16:02:54] Testing sf.net issue 2788233. +34: [16:02:54] done +34: [16:02:54] ------------------------------------- +34: [16:02:54] Testing sf.net issue 3202580. 34: mass! 13.0034 -34: [19:37:05] done -34: [19:37:05] ------------------------------------- -34: [19:37:05] Testing sf.net issue 3316407. -34: [19:37:05] done -34: [19:37:05] ------------------------------------- -34: [19:37:05] Testing sf.net issue 3496759. +34: [16:02:54] done +34: [16:02:54] ------------------------------------- +34: [16:02:54] Testing sf.net issue 3316407. +34: [16:02:54] done +34: [16:02:54] ------------------------------------- +34: [16:02:54] Testing sf.net issue 3496759. 34: smi match: *C *C 34: smi match: **=* **=* 34: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O @@ -18418,13 +18186,6 @@ 34: smi match: O=COC=O O=COC=O 34: smi match: OO OO 34: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F -43: [19:37:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [19:37:05] Unusual charge on atom 0 number of radical electrons set to zero -43: [19:37:05] Unusual charge on atom 0 number of radical electrons set to zero -43: [19:37:05] Unusual charge on atom 0 number of radical electrons set to zero -43: [19:37:05] non-ring atom 0 marked aromatic -43: [19:37:05] non-ring atom 0 marked aromatic -26: ...[19:37:05] Warning: molecule is tagged as 3D, but all Z coords are zero 34: smi match: O=COc1ccc(N(=O)=O)cc1 O=COc1ccc(N(=O)=O)cc1 34: smi match: nnnOC=O nnnOC=O 34: smi match: *=C=N *=C=N @@ -18445,27 +18206,7 @@ 34: smi match: N#CC[OH] N#CC[OH] 34: smi match: N#CC=O N#CC=O 34: smi match: N#CS(=O)=O N#CS(=O)=O -43: =============================================================================== -43: All tests passed (1316 assertions in 75 test cases) -43: -45: =============================================================================== -45: All tests passed (281 assertions in 10 test cases) -45: 34: smi match: CCOP(=O)(C#N)OCC CCOP(=O)(C#N)OCC - 35/208 Test #43: graphmolTestsCatch ..................... Passed 0.08 sec -test 51 - Start 51: pyDepictor - -51: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/testDepictor.py" -51: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/Wrap -51: Test timeout computed to be: 1500 - 36/208 Test #45: graphmolAdjustQueryCatch ............... Passed 0.07 sec -test 52 - Start 52: smiTest1 - -52: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 -52: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse -52: Test timeout computed to be: 1500 34: smi match: N#CN=N N#CN=N 34: smi match: N=NCC=O N=NCC=O 34: smi match: CCCCCCC CCCCCCC @@ -18493,21 +18234,6 @@ 34: smi match: C1CC2CCC(O1)O2 C1CC2CCC(O1)O2 34: smi match: cN(=O)~O cN(=O)~O 34: smi match: *[CH2]N1C(=O)CCC1=O *[CH2]N1C(=O)CCC1=O -48: =============================================================================== -48: All tests passed (8 assertions in 3 test cases) -48: -46: [19:37:05] unable to set wavy bonds for double bonds: 3 -46: [19:37:05] Warning: molecule is tagged as 3D, but all Z coords are zero -46: [19:37:05] Warning: molecule is tagged as 3D, but all Z coords are zero -46: [19:37:05] Warning: molecule is tagged as 3D, but all Z coords are zero -26: [19:37:05] Molecule does not have explicit Hs. Consider calling AddHs() - 37/208 Test #48: moliteratorTestsCatch .................. Passed 0.04 sec -test 53 - Start 53: smiTest2 - -53: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 -53: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse -53: Test timeout computed to be: 1500 34: smi match: N~NC=O N~NC=O 34: smi match: *=N~C *=N~C 34: smi match: CO*(=O)=O CO*(=O)=O @@ -18531,9 +18257,6 @@ 34: smi match: O=CN(O)C=O O=CN(O)C=O 34: smi match: O=CN(S)C=O O=CN(S)C=O 34: smi match: O=CNC=O O=CNC=O -46: [19:37:05] Warning: molecule is tagged as 3D, but all Z coords are zero -46: [19:37:05] Warning: molecule is tagged as 3D, but all Z coords are zero -46: [19:37:05] Warning: molecule is tagged as 3D, but all Z coords are zero 34: smi match: O=CNN=O O=CNN=O 34: smi match: O=CNNC=O O=CNNC=O 34: smi match: O=CNOC=O O=CNOC=O @@ -18546,8 +18269,6 @@ 34: smi match: CN=O CN=O 34: smi match: CS(=O)(=O)O CS(=O)(=O)O 34: smi match: O=C1CCO1 O=C1CCO1 -46: [19:37:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -46: [19:37:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 34: smi match: C=C(S)[SH]=O C=C(S)[SH]=O 34: smi match: C=CCO C=CCO 34: smi match: C=CC=N C=CC=N @@ -18556,39 +18277,7 @@ 34: smi match: C=CC=S C=CC=S 34: smi match: C=CC(=S)S C=CC(=S)S 34: smi match: *C=C(*)C=C *C=C(*)C=C -53: [19:37:05] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' -53: [19:37:05] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -53: [19:37:05] SMILES Parse Error: syntax error while parsing: - -53: [19:37:05] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' -53: [19:37:05] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' -53: [19:37:05] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' -53: [19:37:05] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -53: [19:37:05] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' -53: [19:37:05] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' -53: [19:37:05] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' -53: [19:37:05] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' -53: [19:37:05] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' -53: [19:37:05] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' -53: [19:37:05] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' -53: [19:37:05] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' -50: =============================================================================== -50: All tests passed (65 assertions in 4 test cases) -50: 34: smi match: C=CC=N C=CC=N - 38/208 Test #50: depictorCatch .......................... Passed 0.04 sec -test 54 - Start 54: cxsmilesTest - -54: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest -54: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse -54: Test timeout computed to be: 1500 - 39/208 Test #53: smiTest2 ............................... Passed 0.02 sec -test 55 - Start 55: smaTest1 - -55: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 -55: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse -55: Test timeout computed to be: 1500 34: smi match: *N(*)C=C *N(*)C=C 34: smi match: C=CN(=O)=O C=CN(=O)=O 34: smi match: C=CN(O)=O C=CN(O)=O @@ -18622,16 +18311,6 @@ 34: smi match: *C=N *C=N 34: smi match: N=CC=O N=CC=O 34: smi match: N=CS N=CS -46: =============================================================================== -46: All tests passed (1587 assertions in 50 test cases) -46: - 40/208 Test #46: chiralityTestsCatch .................... Passed 0.09 sec -test 56 - Start 56: smiTestCatch - -56: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -56: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse -56: Test timeout computed to be: 1500 34: smi match: N=C=N N=C=N 34: smi match: N=C=O N=C=O 34: smi match: N=C=S N=C=S @@ -18659,52 +18338,6 @@ 34: smi match: *c1ccccn1 *c1ccccn1 34: smi match: *c1nccccn1 *c1nccccn1 34: smi match: C1COCOC1 C1COCOC1 -49: -49: RDKit 2D -49: -49: 8 9 0 0 0 0 0 0 0 0999 V2000 -49: 1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -49: 0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -49: -0.7500 -1.2990 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -49: -1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -49: -0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -49: 0.7500 1.2990 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -49: 0.2954 0.6125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -49: -0.3828 -0.5621 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -49: 1 2 1 0 -49: 2 3 1 0 -49: 3 4 1 0 -49: 4 5 1 0 -49: 5 6 1 0 -49: 6 7 1 0 -49: 7 8 1 0 -49: 6 1 1 0 -49: 8 3 1 0 -49: M END -49: -49: -49: RDKit 2D -49: -49: 8 9 0 0 0 0 0 0 0 0999 V2000 -49: 1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -49: 0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -49: -0.7500 -1.2990 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -49: -1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -49: -0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -49: 0.7500 1.2990 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -49: -0.4000 0.6928 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -49: -0.8000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -49: 1 2 1 0 -49: 2 3 1 0 -49: 3 4 1 0 -49: 4 5 1 0 -49: 5 6 1 0 -49: 6 7 1 0 -49: 7 8 1 0 -49: 6 1 1 0 -49: 8 3 1 0 -49: M END -49: 34: smi match: C=S C=S 34: smi match: c=S c=S 34: smi match: S=CS S=CS @@ -18718,8 +18351,6 @@ 34: smi match: O=N(O)C[SH](=O)=O O=N(O)C[SH](=O)=O 34: smi match: N#CS N#CS 34: smi match: C=NO C=NO -52: [19:37:05] WARNING: not removing hydrogen atom without neighbors -52: [19:37:05] WARNING: not removing hydrogen atom without neighbors 34: smi match: C=N[SH]=N C=N[SH]=N 34: smi match: O=C(S)S O=C(S)S 34: smi match: N=C(S)S N=C(S)S @@ -18748,14 +18379,6 @@ 34: smi match: O=CC=O O=CC=O 34: smi match: O=CNOC=O O=CNOC=O 34: smi match: O=C1C=CC(=O)C=C1 O=C1C=CC(=O)C=C1 -52: [19:37:05] WARNING: not removing hydrogen atom without neighbors -52: [19:37:05] WARNING: not removing hydrogen atom without neighbors -52: [19:37:05] WARNING: not removing hydrogen atom without neighbors -52: [19:37:05] WARNING: not removing hydrogen atom without neighbors -52: [19:37:05] WARNING: not removing hydrogen atom without neighbors -52: [19:37:05] WARNING: not removing hydrogen atom without neighbors -52: [19:37:05] WARNING: not removing hydrogen atom without neighbors -52: [19:37:05] WARNING: not removing hydrogen atom without neighbors 34: smi match: ONO ONO 34: smi match: ON(~O)~O ON(~O)~O 34: smi match: OC1COC(O)C1 OC1COC(O)C1 @@ -18772,19 +18395,6 @@ 34: smi match: COS(C)(=O)=O COS(C)(=O)=O 34: smi match: C1CO1 C1CO1 34: smi match: *c1-c-c-ccN1 *c1-c-c-ccN1 -52: [19:37:05] WARNING: not removing hydrogen atom without neighbors -52: [19:37:05] Invalid chiral specification on atom 0 -52: [19:37:05] Invalid chiral specification on atom 0 -52: [19:37:05] Invalid chiral specification on atom 0 -52: [19:37:05] Invalid chiral specification on atom 0 -52: [19:37:05] Invalid chiral specification on atom 0 - 41/208 Test #54: cxsmilesTest ........................... Passed 0.03 sec -test 57 - Start 57: nontetrahedralCatch - -57: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch -57: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse -57: Test timeout computed to be: 1500 34: smi match: *C(*)=C *C(*)=C 34: smi match: N#[NH+] N#[NH+] 34: smi match: C#NO C#NO @@ -18810,10 +18420,7 @@ 34: smi match: COC(C)=N COC(C)=N 34: smi match: C=C=C C=C=C 34: smi match: *C(=O)OC=O *C(=O)OC=O -56: [19:37:05] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -56: [19:37:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 34: smi match: C=CC#N C=CC#N -56: [19:37:05] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' 34: smi match: C=CC=O C=CC=O 34: smi match: CC=CC(C)=O CC=CC(C)=O 34: smi match: CC=CC(=O)OCC CC=CC(=O)OCC @@ -18857,7 +18464,6 @@ 34: smi match: *C(*)NCN(*)* *C(*)NCN(*)* 34: smi match: *OCC#N *OCC#N 34: smi match: **C=C **C=C -56: [19:37:05] SMARTS Parse Error: unclosed ring for input: 'C1C' 34: smi match: C=C[O-] C=C[O-] 34: smi match: C=CO C=CO 34: smi match: * * @@ -18873,20 +18479,12 @@ 34: smi match: *C* *C* 34: smi match: * * 34: smi match: C[nH3+] C[nH3+] -56: [19:37:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -56: [19:37:05] SMARTS Parse Error: syntax error while parsing: C)foo -56: [19:37:05] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' -56: [19:37:05] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| -56: [19:37:05] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' 34: smi match: cC(=N)[NH2] cC(=N)[NH2] 34: smi match: O=CN[OH] O=CN[OH] 34: smi match: NN NN 34: smi match: * * 34: smi match: *OP(=O)O* *OP(=O)O* -56: [19:37:05] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' -52: [19:37:05] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' 34: smi match: * * -52: [19:37:05] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' 34: smi match: * * 34: smi match: * * 34: smi match: *N=C(*)* *N=C(*)* @@ -18908,7 +18506,6 @@ 34: smi match: cCC(=O)[OH] cCC(=O)[OH] 34: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH] 34: smi match: CC(=O)C(=O)[OH] CC(=O)C(=O)[OH] -57: [19:37:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 34: smi match: C=CC(=O)[OH] C=CC(=O)[OH] 34: smi match: N#CC(=O)[OH] N#CC(=O)[OH] 34: smi match: O=C([OH])CN(~O)~O O=C([OH])CN(~O)~O @@ -18933,18 +18530,17 @@ 34: smi match: N~N~N N~N~N 34: smi match: *N=N* *N=N* 34: smi match: *CC[OH] *CC[OH] -57: [19:37:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 34: smi match: *CC[OH] *CC[OH] 34: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] 34: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] 34: smi match: *CCC(=O)[OH] *CCC(=O)[OH] 34: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] 34: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O +32: [16:02:54] Maximum BFS search size exceeded. +32: This is likely due to a highly symmetric fused ring system. 34: smi match: *OC(*)=O *OC(*)=O 34: smi match: *C(=O)[OH] *C(=O)[OH] 34: smi match: O=C[OH] O=C[OH] -57: [19:37:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [19:37:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 34: smi match: *OC(=O)O* *OC(=O)O* 34: smi match: * * 34: smi match: *OC(=O)Cl *OC(=O)Cl @@ -18953,9 +18549,7 @@ 34: smi match: SS SS 34: smi match: * * 34: smi match: *=* *=* -57: [19:37:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 34: smi match: *=* *=* -57: [19:37:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 34: smi match: *=* *=* 34: smi match: *=* *=* 34: smi match: C1CO1 C1CO1 @@ -18973,8 +18567,6 @@ 34: smi match: CN=C=S CN=C=S 34: smi match: *OC(*)(*)O* *OC(*)(*)O* 34: smi match: *C(*)=O *C(*)=O -57: [19:37:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [19:37:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 34: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C 34: smi match: *~*=O *~*=O 34: smi match: *~*=O *~*=O @@ -18994,22 +18586,16 @@ 34: smi match: O=P(~O)~O O=P(~O)~O 34: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O 34: smi match: C[NH2] C[NH2] +32: F/C=C/Cl +32: [H]/C(F)=C(/[H])Cl 34: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 +32: F/C=C/Cl +32: F/C=C/Cl +32: C/C(F)=C(/C)Cl 34: smi match: * * -57: [19:37:05] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. -57: =============================================================================== -57: All tests passed (308 assertions in 9 test cases) -57: 34: smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 34: smi match: CS(C)~O CS(C)~O 34: smi match: CS(C)(~O)~O CS(C)(~O)~O - 42/208 Test #57: nontetrahedralCatch .................... Passed 0.07 sec -test 58 - Start 58: fileParsersTest1 - -58: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -58: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers -58: Test timeout computed to be: 1500 34: smi match: CS(N)(~O)~O CS(N)(~O)~O 34: smi match: CS([OH])(~O)~O CS([OH])(~O)~O 34: smi match: COS(C)(~O)~O COS(C)(~O)~O @@ -19025,369 +18611,1086 @@ 34: smi match: * * 34: smi match: ***** ***** 34: smi match: NC(N)=O NC(N)=O -34: [19:37:05] done -34: [19:37:05] ------------------------------------- -34: [19:37:05] Testing sf.net issue 280. -34: [19:37:05] done -34: [19:37:05] ------------------------------------- -34: [19:37:05] Testing sf.net issue 285. -34: [19:37:05] done -34: [19:37:05] done -34: [19:37:05] done -34: [19:37:05] done -34: [19:37:05] done -34: [19:37:05] done -34: [19:37:05] done -34: [19:37:05] ------------------------------------- -34: [19:37:05] Testing Github2441: Add RDProps interface to Conformers. -34: [19:37:05] done -34: [19:37:05] ------------------------------------- -34: [19:37:05] Testing Issue2510: Pickle Confs as double. -34: [19:37:05] done -34: [19:37:05] ------------------------------------- -34: [19:37:05] Testing Github #2465: Negative atom-map numbers cause depickling to fail. -34: [19:37:05] done -34: [19:37:05] ------------------------------------- -34: [19:37:05] Testing loading pickled mols with conformers -34: [19:37:05] done -34: [19:37:05] ------------------------------------- -34: [19:37:05] Testing conformer reading/writing options -34: [19:37:05] done -34: [19:37:05] ------------------------------------- -34: [19:37:05] Testing property reading options -34: [19:37:05] done -34: [19:37:05] ------------------------------------- -34: [19:37:05] Testing property reading options -34: [19:37:05] done -34: [19:37:05] ------------------------------------- -34: [19:37:05] Testing boost::serialization integration -34: [19:37:05] done - 43/208 Test #34: graphmoltestPickler .................... Passed 0.29 sec +34: [16:02:54] done +34: [16:02:54] ------------------------------------- +34: [16:02:54] Testing sf.net issue 280. +34: [16:02:54] done +34: [16:02:54] ------------------------------------- +34: [16:02:54] Testing sf.net issue 285. +34: [16:02:54] done +34: [16:02:54] done +34: [16:02:54] done +34: [16:02:54] done +34: [16:02:54] done +34: [16:02:54] done +34: [16:02:54] done +34: [16:02:54] ------------------------------------- +34: [16:02:54] Testing Github2441: Add RDProps interface to Conformers. +34: [16:02:54] done +34: [16:02:54] ------------------------------------- +34: [16:02:54] Testing Issue2510: Pickle Confs as double. +34: [16:02:54] done +34: [16:02:54] ------------------------------------- +34: [16:02:54] Testing Github #2465: Negative atom-map numbers cause depickling to fail. +34: [16:02:54] done +34: [16:02:54] ------------------------------------- +34: [16:02:54] Testing loading pickled mols with conformers +34: [16:02:54] done +34: [16:02:54] ------------------------------------- +34: [16:02:54] Testing conformer reading/writing options +34: [16:02:54] done +34: [16:02:54] ------------------------------------- +34: [16:02:54] Testing property reading options +34: [16:02:54] done +34: [16:02:54] ------------------------------------- +34: [16:02:54] Testing property reading options +34: [16:02:54] done +34: [16:02:54] ------------------------------------- +34: [16:02:54] Testing boost::serialization integration +34: [16:02:54] done + 28/208 Test #34: graphmoltestPickler .................... Passed 0.37 sec +test 35 + Start 35: graphmoltestPicklerGlobalSetting + +35: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting +35: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol +35: Test timeout computed to be: 1500 + 29/208 Test #32: graphmolMolOpsTest ..................... Passed 1.15 sec +test 36 + Start 36: graphmolIterTest + +36: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/graphmolIterTest +36: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol +36: Test timeout computed to be: 1500 +3: dynamic RDAny:0.59426 s +3: static RDValue:1e-06 s +35: [16:02:54] done + 30/208 Test #35: graphmoltestPicklerGlobalSetting ....... Passed 0.03 sec +test 37 + Start 37: hanoiTest + +37: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/hanoiTest +37: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol +37: Test timeout computed to be: 1500 + 31/208 Test #36: graphmolIterTest ....................... Passed 0.03 sec +test 38 + Start 38: graphmolMemTest1 + +38: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/graphmolMemTest1 +38: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol +38: Test timeout computed to be: 1500 + 32/208 Test #38: graphmolMemTest1 ....................... Passed 0.01 sec +test 39 + Start 39: resMolSupplierTest + +39: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/resMolSupplierTest +39: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol +39: Test timeout computed to be: 1500 +3: dynamic RDValue:0.065479 s +3: deleted! +3: [16:02:54] ------------------------------------- +3: [16:02:54] Testing String Pickle Roundtrips. +3: [16:02:54] done +3: [16:02:54] ------------------------------------- +3: [16:02:54] Testing conversion of vect to string. +3: [16:02:54] done +3: [16:02:54] ------------------------------------- +3: [16:02:54] Testing returning const references. +3: [16:02:54] any cast +3: [16:02:54] done: 0.004221 300000 +3: [16:02:54] copy +3: [16:02:54] done: 0.002485 300000 +3: [16:02:54] ref +3: [16:02:54] done: 0.002548 300000 +3: [16:02:54] dict +3: [16:02:54] done: 0.006318 300000 +3: [16:02:54] ref with hasVal +3: [16:02:54] done: 0.005165 300000 +3: [16:02:54] done +3: [16:02:54] ------------------------------------- +3: [16:02:54] Testing dict update. +3: [16:02:54] done +3: deleted! +3: deleted! +3: deleted! +3: deleted! +3: deleted! +3: deleted! + 33/208 Test #3: testDict ............................... Passed 2.56 sec +test 40 + Start 40: molBundleTest + +40: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/molBundleTest +40: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol +40: Test timeout computed to be: 1500 + 34/208 Test #40: molBundleTest .......................... Passed 0.03 sec +test 41 + Start 41: testSGroup + +41: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/testSGroup +41: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol +41: Test timeout computed to be: 1500 + 35/208 Test #41: testSGroup ............................. Passed 0.05 sec +test 42 + Start 42: test-valgrind + +42: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/test-valgrind +42: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol +42: Test timeout computed to be: 1500 + 36/208 Test #42: test-valgrind .......................... Passed 0.03 sec +test 43 + Start 43: graphmolTestsCatch + +43: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +43: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol +43: Test timeout computed to be: 1500 +43: [16:02:54] WARNING: not removing hydrogen atom without neighbors +43: [16:02:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [16:02:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [16:02:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [16:02:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [16:02:54] Explicit valence for atom # 1 N, 5, is greater than permitted +43: [16:02:54] Explicit valence for atom # 1 N, 6, is greater than permitted +43: [16:02:54] Explicit valence for atom # 1 N, 5, is greater than permitted +43: [16:02:54] Explicit valence for atom # 1 N, 5, is greater than permitted +43: [16:02:54] Explicit valence for atom # 2 O, 3, is greater than permitted +43: [16:02:54] Explicit valence for atom # 2 O, 3, is greater than permitted +43: [16:02:54] non-ring atom 2 marked aromatic +43: [16:02:54] non-ring atom 2 marked aromatic +43: [16:02:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [16:02:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [16:02:54] Can't kekulize mol. Unkekulized atoms: 1 2 3 +43: [16:02:54] Can't kekulize mol. Unkekulized atoms: 1 2 3 +43: [16:02:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 +43: [16:02:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 +43: [16:02:54] Explicit valence for atom # 1 O, 3, is greater than permitted +43: [16:02:54] Explicit valence for atom # 4 F, 2, is greater than permitted +43: [16:02:54] Can't kekulize mol. Unkekulized atoms: 6 7 8 +43: [16:02:54] Explicit valence for atom # 1 C, 5, is greater than permitted +43: [16:02:54] WARNING: not removing hydrogen atom with dummy atom neighbors +43: [16:02:54] WARNING: not removing hydrogen atom with dummy atom neighbors +43: [16:02:54] WARNING: not removing hydrogen atom with wedged bond +43: [16:02:54] WARNING: not removing hydrogen atom without neighbors +43: [16:02:54] WARNING: not removing hydrogen atom without neighbors +43: [16:02:54] WARNING: not removing hydrogen atom without neighbors +43: [16:02:54] WARNING: not removing hydrogen atom without neighbors +43: [16:02:54] Unreasonable formal charge on hydrogen # 0. +43: [16:02:55] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() +43: [16:02:55] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() +43: [16:02:55] +43: +43: **** +43: Pre-condition Violation +43: no atom +43: Violation occurred on line 183 in file ./Code/GraphMol/ROMol.cpp +43: Failed Expression: at +43: **** +43: +43: [16:02:55] +43: +43: **** +43: Pre-condition Violation +43: atom not associated with a molecule +43: Violation occurred on line 184 in file ./Code/GraphMol/ROMol.cpp +43: Failed Expression: at->hasOwningMol() +43: **** +43: +43: [16:02:55] +43: +43: **** +43: Pre-condition Violation +43: atom not associated with this molecule +43: Violation occurred on line 185 in file ./Code/GraphMol/ROMol.cpp +43: Failed Expression: &at->getOwningMol() == this +43: **** +43: +43: [16:02:55] +43: +43: **** +43: Pre-condition Violation +43: no atom +43: Violation occurred on line 382 in file ./Code/GraphMol/ROMol.cpp +43: Failed Expression: at +43: **** +43: +43: [16:02:55] +43: +43: **** +43: Pre-condition Violation +43: atom not associated with a molecule +43: Violation occurred on line 383 in file ./Code/GraphMol/ROMol.cpp +43: Failed Expression: at->hasOwningMol() +43: **** +43: +43: [16:02:55] +43: +43: **** +43: Pre-condition Violation +43: atom not associated with this molecule +43: Violation occurred on line 384 in file ./Code/GraphMol/ROMol.cpp +43: Failed Expression: &at->getOwningMol() == this +43: **** +43: +43: [16:02:55] +43: +43: **** +43: Pre-condition Violation +43: no atom +43: Violation occurred on line 390 in file ./Code/GraphMol/ROMol.cpp +43: Failed Expression: at +43: **** +43: +43: [16:02:55] +43: +43: **** +43: Pre-condition Violation +43: atom not associated with a molecule +43: Violation occurred on line 391 in file ./Code/GraphMol/ROMol.cpp +43: Failed Expression: at->hasOwningMol() +43: **** +43: +43: [16:02:55] +43: +43: **** +43: Pre-condition Violation +43: atom not associated with this molecule +43: Violation occurred on line 392 in file ./Code/GraphMol/ROMol.cpp +43: Failed Expression: &at->getOwningMol() == this +43: **** +43: +43: [16:02:55] +43: +43: **** +43: Pre-condition Violation +43: null atom passed in +43: Violation occurred on line 406 in file ./Code/GraphMol/ROMol.cpp +43: Failed Expression: atom_pin +43: **** +43: +43: [16:02:55] +43: +43: **** +43: Pre-condition Violation +43: cannot take ownership of an atom which already has an owner +43: Violation occurred on line 407 in file ./Code/GraphMol/ROMol.cpp +43: Failed Expression: !takeOwnership || !atom_pin->hasOwningMol() || &atom_pin->getOwningMol() == this +43: **** +43: +43: [16:02:55] +43: +43: **** +43: Pre-condition Violation +43: cannot take ownership of an bond which already has an owner +43: Violation occurred on line 433 in file ./Code/GraphMol/ROMol.cpp +43: Failed Expression: !takeOwnership || !bond_pin->hasOwningMol() || &bond_pin->getOwningMol() == this +43: **** +43: +43: [16:02:55] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [16:02:55] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [16:02:55] WARNING: not removing hydrogen atom without neighbors +43: [16:02:55] Explicit valence for atom # 1 F greater than permitted +43: [16:02:55] +43: +43: **** +43: Pre-condition Violation +43: plain atoms have no Query +43: Violation occurred on line 625 in file ./Code/GraphMol/Atom.cpp +43: Failed Expression: 0 +43: **** +43: +43: [16:02:55] +43: +43: **** +43: Pre-condition Violation +43: plain atoms have no Query +43: Violation occurred on line 630 in file ./Code/GraphMol/Atom.cpp +43: Failed Expression: 0 +43: **** +43: +43: [16:02:55] +43: +43: **** +43: Pre-condition Violation +43: plain bonds have no Query +43: Violation occurred on line 206 in file ./Code/GraphMol/Bond.cpp +43: Failed Expression: 0 +43: **** +43: +43: [16:02:55] +43: +43: **** +43: Pre-condition Violation +43: plain bonds have no query +43: Violation occurred on line 227 in file ./Code/GraphMol/Bond.cpp +43: Failed Expression: 0 +43: **** +43: +43: [16:02:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [16:02:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [16:02:55] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +43: [16:02:55] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +43: [16:02:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [16:02:55] Unusual charge on atom 0 number of radical electrons set to zero +43: [16:02:55] Unusual charge on atom 0 number of radical electrons set to zero +43: [16:02:55] Unusual charge on atom 0 number of radical electrons set to zero +43: [16:02:55] non-ring atom 0 marked aromatic +43: [16:02:55] non-ring atom 0 marked aromatic +43: =============================================================================== +43: All tests passed (1316 assertions in 75 test cases) +43: + 37/208 Test #43: graphmolTestsCatch ..................... Passed 0.08 sec +test 44 + Start 44: graphmolSGroupCatch + +44: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/graphmolSGroupCatch +44: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol +44: Test timeout computed to be: 1500 +44: =============================================================================== +44: All tests passed (120 assertions in 6 test cases) +44: + 38/208 Test #44: graphmolSGroupCatch .................... Passed 0.03 sec +test 45 + Start 45: graphmolAdjustQueryCatch + +45: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch +45: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol +45: Test timeout computed to be: 1500 +45: =============================================================================== +45: All tests passed (281 assertions in 10 test cases) +45: + 39/208 Test #45: graphmolAdjustQueryCatch ............... Passed 0.07 sec +test 46 + Start 46: chiralityTestsCatch + +46: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/chiralityTestsCatch +46: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol +46: Test timeout computed to be: 1500 +46: [16:02:55] unable to set wavy bonds for double bonds: 3 +46: [16:02:55] Warning: molecule is tagged as 3D, but all Z coords are zero +46: [16:02:55] Warning: molecule is tagged as 3D, but all Z coords are zero +46: [16:02:55] Warning: molecule is tagged as 3D, but all Z coords are zero +46: [16:02:55] Warning: molecule is tagged as 3D, but all Z coords are zero +46: [16:02:55] Warning: molecule is tagged as 3D, but all Z coords are zero +46: [16:02:55] Warning: molecule is tagged as 3D, but all Z coords are zero +46: [16:02:55] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +46: [16:02:55] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +46: =============================================================================== +46: All tests passed (1587 assertions in 50 test cases) +46: + 40/208 Test #46: chiralityTestsCatch .................... Passed 0.10 sec +test 47 + Start 47: canonTestsCatch + +47: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/canonTestsCatch +47: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol +47: Test timeout computed to be: 1500 +47: 2 6 8 4 9 0 7 3 5 1 +47: 1 5 7 3 9 0 8 4 6 2 +47: 1 5 7 3 9 0 8 4 6 2 +47: 1 5 7 3 9 0 8 4 6 2 +47: =============================================================================== +47: All tests passed (47 assertions in 2 test cases) +47: + 41/208 Test #47: canonTestsCatch ........................ Passed 0.03 sec +test 48 + Start 48: moliteratorTestsCatch + +48: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/moliteratorTestsCatch +48: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol +48: Test timeout computed to be: 1500 +48: =============================================================================== +48: All tests passed (8 assertions in 3 test cases) +48: + 42/208 Test #48: moliteratorTestsCatch .................. Passed 0.04 sec +test 49 + Start 49: testDepictor + +49: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/testDepictor +49: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor +49: Test timeout computed to be: 1500 +49: +49: RDKit 2D +49: +49: 8 9 0 0 0 0 0 0 0 0999 V2000 +49: 1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +49: 0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +49: -0.7500 -1.2990 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +49: -1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +49: -0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +49: 0.7500 1.2990 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +49: 0.2954 0.6125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +49: -0.3828 -0.5621 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +49: 1 2 1 0 +49: 2 3 1 0 +49: 3 4 1 0 +49: 4 5 1 0 +49: 5 6 1 0 +49: 6 7 1 0 +49: 7 8 1 0 +49: 6 1 1 0 +49: 8 3 1 0 +49: M END +49: +49: +49: RDKit 2D +49: +49: 8 9 0 0 0 0 0 0 0 0999 V2000 +49: 1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +49: 0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +49: -0.7500 -1.2990 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +49: -1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +49: -0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +49: 0.7500 1.2990 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +49: -0.4000 0.6928 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +49: -0.8000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +49: 1 2 1 0 +49: 2 3 1 0 +49: 3 4 1 0 +49: 4 5 1 0 +49: 5 6 1 0 +49: 6 7 1 0 +49: 7 8 1 0 +49: 6 1 1 0 +49: 8 3 1 0 +49: M END +49: +49: [16:02:55] Warning: stereochemistry around double bond may be incorrect in depiction. + 43/208 Test #49: testDepictor ........................... Passed 0.48 sec +test 50 + Start 50: depictorCatch + +50: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/depictorCatch +50: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor +50: Test timeout computed to be: 1500 +50: =============================================================================== +50: All tests passed (65 assertions in 4 test cases) +50: + 44/208 Test #50: depictorCatch .......................... Passed 0.04 sec +test 51 + Start 51: pyDepictor + +51: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/testDepictor.py" +51: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/Wrap +51: Test timeout computed to be: 1500 +51: ....E..... +51: ====================================================================== +51: ERROR: test5SamplingMimic3D (__main__.TestCase.test5SamplingMimic3D) +51: ---------------------------------------------------------------------- +51: Traceback (most recent call last): +51: File "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/testDepictor.py", line 188, in test5SamplingMimic3D +51: dmat3D = getDistMat(mol) +51: ^^^^^^^^^^^^^^^ +51: File "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/testDepictor.py", line 31, in getDistMat +51: res = np.zeros(nl, np.float) +51: ^^^^^^^^ +51: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ +51: raise AttributeError(__former_attrs__[attr]) +51: AttributeError: module 'numpy' has no attribute 'float'. +51: `np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here. +51: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: +51: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations +51: +51: ---------------------------------------------------------------------- +51: Ran 10 tests in 0.258s +51: +51: FAILED (errors=1) + 45/208 Test #51: pyDepictor .............................***Failed 0.55 sec +....E..... +====================================================================== +ERROR: test5SamplingMimic3D (__main__.TestCase.test5SamplingMimic3D) +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/testDepictor.py", line 188, in test5SamplingMimic3D + dmat3D = getDistMat(mol) + ^^^^^^^^^^^^^^^ + File "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/testDepictor.py", line 31, in getDistMat + res = np.zeros(nl, np.float) + ^^^^^^^^ + File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ + raise AttributeError(__former_attrs__[attr]) +AttributeError: module 'numpy' has no attribute 'float'. +`np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here. +The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: + https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations + +---------------------------------------------------------------------- +Ran 10 tests in 0.258s + +FAILED (errors=1) + +test 52 + Start 52: smiTest1 + +52: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 +52: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse +52: Test timeout computed to be: 1500 +52: [16:02:56] WARNING: not removing hydrogen atom without neighbors +52: [16:02:56] WARNING: not removing hydrogen atom without neighbors +52: [16:02:56] WARNING: not removing hydrogen atom without neighbors +52: [16:02:56] WARNING: not removing hydrogen atom without neighbors +52: [16:02:56] WARNING: not removing hydrogen atom without neighbors +52: [16:02:56] WARNING: not removing hydrogen atom without neighbors +52: [16:02:56] WARNING: not removing hydrogen atom without neighbors +52: [16:02:56] WARNING: not removing hydrogen atom without neighbors +52: [16:02:56] WARNING: not removing hydrogen atom without neighbors +52: [16:02:56] WARNING: not removing hydrogen atom without neighbors +52: [16:02:56] WARNING: not removing hydrogen atom without neighbors +52: [16:02:56] Invalid chiral specification on atom 0 +52: [16:02:56] Invalid chiral specification on atom 0 +52: [16:02:56] Invalid chiral specification on atom 0 +52: [16:02:56] Invalid chiral specification on atom 0 +52: [16:02:56] Invalid chiral specification on atom 0 +52: [16:02:56] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' +52: [16:02:56] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' +52: --C1CCC2(CC1)CCCCC2CCC1CCCC1 +52: smi: ClC1CCCCC1 +52: smi: ClC1CCCCC1 +52: smi: ClC1CCCCC1Br +52: smi: c1ccccc1 +52: smi: c1ccncc1 +52: smi: c1cc[nH]c1 +52: smi: c1cc[nH]c1 +52: smi: c1cc[pH]c1 +52: CbC(aC)aC +52: CaC(bC)aC +52: CbC(bC)aC +52: O.C +52: 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 +52: [16:02:56] SMILES Parse Error: syntax error while parsing: c%()ccccc%() +52: [16:02:56] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' +52: [16:02:56] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) +52: [16:02:56] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' +52: [16:02:56] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' +52: [16:02:56] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' +52: [16:02:56] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +52: [16:02:56] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +52: [16:02:56] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +52: [16:02:56] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +52: [16:02:56] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +52: [16:02:56] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +52: [16:02:56] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +52: [16:02:56] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +52: [16:02:56] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +52: [16:02:56] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +52: [16:02:56] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +52: [16:02:56] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +52: C=c1s/c2n(c1=O)CCCCCCC\N=2 +52: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 +52: [16:02:56] SMILES Parse Error: extra close parentheses while parsing: C) +52: [16:02:56] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' + 46/208 Test #52: smiTest1 ............................... Passed 0.28 sec +test 53 + Start 53: smiTest2 + +53: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 +53: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse +53: Test timeout computed to be: 1500 +53: [16:02:56] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' +53: [16:02:56] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +53: [16:02:56] SMILES Parse Error: syntax error while parsing: - +53: [16:02:56] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' +53: [16:02:56] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' +53: [16:02:56] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' +53: [16:02:56] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +53: [16:02:56] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' +53: [16:02:56] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' +53: [16:02:56] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' +53: [16:02:56] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' +53: [16:02:56] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' +53: [16:02:56] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' +53: [16:02:56] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' +53: [16:02:56] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' + 47/208 Test #53: smiTest2 ............................... Passed 0.02 sec +test 54 + Start 54: cxsmilesTest + +54: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest +54: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse +54: Test timeout computed to be: 1500 + 48/208 Test #54: cxsmilesTest ........................... Passed 0.03 sec +test 55 + Start 55: smaTest1 + +55: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 +55: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse +55: Test timeout computed to be: 1500 +55: [16:02:56] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC +55: [16:02:56] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' +55: [16:02:56] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON +55: [16:02:56] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' +55: [16:02:56] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +55: [16:02:56] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged + 49/208 Test #55: smaTest1 ............................... Passed 0.20 sec +test 56 + Start 56: smiTestCatch + +56: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +56: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse +56: Test timeout computed to be: 1500 +56: [16:02:56] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +56: [16:02:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +56: [16:02:56] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' +56: [16:02:56] SMARTS Parse Error: unclosed ring for input: 'C1C' +56: [16:02:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +56: [16:02:56] SMARTS Parse Error: syntax error while parsing: C)foo +56: [16:02:56] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' +56: [16:02:56] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| +56: [16:02:56] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' +56: [16:02:56] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' +56: [16:02:57] w block attempts to set wedging on bond 0 more than once. +56: [16:02:57] improperly formatted w block +56: [16:02:57] atom 3 is not associated with bond 1 in w block +56: =============================================================================== +56: All tests passed (969 assertions in 49 test cases) +56: + 50/208 Test #56: smiTestCatch ........................... Passed 0.15 sec +test 57 + Start 57: nontetrahedralCatch + +57: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch +57: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse +57: Test timeout computed to be: 1500 +57: [16:02:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +25: Checking against /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +57: [16:02:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [16:02:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [16:02:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [16:02:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [16:02:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [16:02:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [16:02:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [16:02:57] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. +57: =============================================================================== +57: All tests passed (308 assertions in 9 test cases) +57: + 51/208 Test #57: nontetrahedralCatch .................... Passed 0.07 sec +test 58 + Start 58: fileParsersTest1 + +58: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +58: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers +58: Test timeout computed to be: 1500 +58: *************************************** +58: *************************************** +58: [16:02:57] bond with order 0 found on line 7. This is not part of the MDL specification. +58: [16:02:57] unrecognized query bond type, 9, found on line 7. Using an "any" query. +58: [16:02:57] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +58: [16:02:57] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +58: [16:02:57] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [16:02:57] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [16:02:57] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [16:02:57] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [16:02:57] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [16:02:57] Warning: molecule is tagged as 3D, but all Z coords are zero +58: generating smiles +58: 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 +58: converting back +58: check isomorphism +25: All 191 tests passed +25: +25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... +58: [16:02:58] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [16:02:58] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [16:02:58] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [16:02:58] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [16:02:58] deprecated group abbreviation ignored on line 24 +58: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +58: [16:02:58] +58: +58: **** +58: Post-condition Violation +58: Element 'Mv' not found +58: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +58: Failed Expression: anum > -1 +58: **** +58: +11: ....F............. +11: ====================================================================== +11: FAIL: test11BulkNeighbors (__main__.TestCase.test11BulkNeighbors) +11: ---------------------------------------------------------------------- +11: Traceback (most recent call last): +11: File "/build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/testBV.py", line 257, in test11BulkNeighbors +11: self.assertEqual(tgts,nbrs) +11: AssertionError: Lists differ: [(816[179 chars]8), (577, 0.6609642301710731), (37, 0.67550702[32 chars]214)] != [(816[179 chars]8), (928, 0.6609642301710731), (37, 0.67550702[32 chars]214)] +11: +11: First differing element 7: +11: (577, 0.6609642301710731) +11: (928, 0.6609642301710731) +11: +11: [(816, 0.6759259259259259), +11: (115, 0.6597542242703534), +11: (118, 0.6746522411128284), +11: (853, 0.675095785440613), +11: (179, 0.6687402799377916), +11: (686, 0.665351223362273), +11: (668, 0.6715610510046368), +11: - (577, 0.6609642301710731), +11: ? ^^^ +11: +11: + (928, 0.6609642301710731), +11: ? ^^^ +11: +11: (37, 0.6755070202808112), +11: (907, 0.6622568093385214)] +11: +11: ---------------------------------------------------------------------- +11: Ran 18 tests in 5.895s +11: +11: FAILED (failures=1) + 52/208 Test #11: pyBV ...................................***Failed 6.37 sec +....F............. +====================================================================== +FAIL: test11BulkNeighbors (__main__.TestCase.test11BulkNeighbors) +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/testBV.py", line 257, in test11BulkNeighbors + self.assertEqual(tgts,nbrs) +AssertionError: Lists differ: [(816[179 chars]8), (577, 0.6609642301710731), (37, 0.67550702[32 chars]214)] != [(816[179 chars]8), (928, 0.6609642301710731), (37, 0.67550702[32 chars]214)] + +First differing element 7: +(577, 0.6609642301710731) +(928, 0.6609642301710731) + + [(816, 0.6759259259259259), + (115, 0.6597542242703534), + (118, 0.6746522411128284), + (853, 0.675095785440613), + (179, 0.6687402799377916), + (686, 0.665351223362273), + (668, 0.6715610510046368), +- (577, 0.6609642301710731), +? ^^^ + ++ (928, 0.6609642301710731), +? ^^^ + + (37, 0.6755070202808112), + (907, 0.6622568093385214)] + +---------------------------------------------------------------------- +Ran 18 tests in 5.895s + +FAILED (failures=1) + test 59 Start 59: testMolSupplier 59: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 59: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 59: Test timeout computed to be: 1500 -26: [19:37:05] -26: -26: **** -26: Invariant Violation -26: bad direction in linearSearch -26: Violation occurred on line 240 in file ./Code/Numerics/Optimizer/BFGSOpt.h -26: Failed Expression: status >= 0 -26: **** -26: -56: [19:37:05] w block attempts to set wedging on bond 0 more than once. -56: [19:37:05] improperly formatted w block -59: [19:37:05] +59: [16:02:58] 59: ----------------------------------------- -56: [19:37:05] atom 3 is not associated with bond 1 in w block -56: =============================================================================== -56: All tests passed (969 assertions in 49 test cases) -56: - 44/208 Test #56: smiTestCatch ........................... Passed 0.13 sec +59: [16:02:58] +59: +59: **** +59: Invariant Violation +59: bad prop value +59: Violation occurred on line 157 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp +59: Failed Expression: nSwaps < 2 +59: **** +59: +59: [16:02:58] Finished: testMolSup() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: [16:02:58] Finished: testRandMolSup() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: [16:02:58] Finished: testSmilesSup() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: [16:02:58] ------------------------------------------------------ +59: [16:02:58] SMILES Parse Error: syntax error while parsing: fail +59: [16:02:58] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +59: [16:02:58] ERROR: Smiles parse error on line 3 +59: [16:02:58] ERROR: Cannot create molecule from : 'fail' +59: [16:02:58] ------------------------------------------------------ +59: [16:02:58] ------------------------------------------------------ +59: [16:02:58] >>> This may result in an infinite loop. It should finish almost immediately: +59: [16:02:58] <<< done. +59: [16:02:58] Finished: testSmilesSupFromText() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: [16:02:58] Finished: testSmilesWriter() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: [16:02:58] Finished: testSDWriter() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: [16:02:58] Finished: testSDSupplierEnding() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: [16:02:58] Finished: testSuppliersEmptyFile() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: [16:02:58] Finished: testCisTrans() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: [16:02:58] Finished: testStereoRound() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: [16:02:58] Finished: testIssue226() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: [16:02:58] Finished: testTDTSupplier1() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: [16:02:58] Finished: testTDTSupplier2() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: [16:02:58] Finished: testTDTSupplier3() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: [16:02:58] Finished: testSDSupplierFromText() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: [16:02:58] ERROR: Problems encountered parsing data fields +59: [16:02:58] ERROR: moving to the beginning of the next molecule +59: [16:02:58] ERROR: Problems encountered parsing data fields +59: [16:02:58] ERROR: moving to the beginning of the next molecule +59: [16:02:58] Spurious data before the first property will be ignored +59: [16:02:58] Property will be truncated after the first blank line +59: [16:02:58] Property will be truncated after the first blank line +59: [16:02:58] Property will be truncated after the first blank line +59: [16:02:58] Finished: testSDSupplierStrLax1() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: [16:02:58] ERROR: Problems encountered parsing data fields +59: [16:02:58] ERROR: moving to the beginning of the next molecule +59: [16:02:58] Property will be truncated after the first blank line +59: [16:02:58] Finished: testSDSupplierStrLax2() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: [16:02:58] ERROR: Problems encountered parsing data fields +59: [16:02:58] ERROR: moving to the beginning of the next molecule +59: [16:02:58] ERROR: Problems encountered parsing data fields +59: [16:02:58] ERROR: moving to the beginning of the next molecule +59: [16:02:58] Spurious data before the first property will be ignored +59: [16:02:58] Property will be truncated after the first blank line +59: [16:02:58] Property will be truncated after the first blank line +59: [16:02:58] Property will be truncated after the first blank line +59: [16:02:58] Finished: testSDSupplierFromTextStrLax1() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: [16:02:58] ERROR: Problems encountered parsing data fields +59: [16:02:58] ERROR: moving to the beginning of the next molecule +59: [16:02:58] Property will be truncated after the first blank line +59: [16:02:58] Finished: testSDSupplierFromTextStrLax2() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: [16:02:58] Finished: testIssue265() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: [16:02:58] ERROR: End of data field name not found +59: [16:02:58] ERROR: moving to the beginning of the next molecule +59: [16:02:58] Explicit valence for atom # 0 F, 2, is greater than permitted +59: [16:02:58] ERROR: Could not sanitize molecule ending on line 16 +59: [16:02:58] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted +59: [16:02:58] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 +59: [16:02:58] ERROR: moving to the beginning of the next molecule +59: [16:02:58] ERROR: Bond line too short: 'M END' on line 18 +59: [16:02:58] ERROR: moving to the beginning of the next molecule +59: [16:02:58] Finished: testSDErrorHandling() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: [16:02:58] Finished: testIssue381() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: [16:02:58] Finished: testSetStreamIndices() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: [16:02:58] Finished: testMixIterAndRandom() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: build: +59: [16:02:58] Finished: testRemoveHs() +59: [16:02:58] ----------------------------------------- +59: +59: [16:02:58] ----------------------------------------- +59: [16:02:59] Finished: testGetItemText() +59: [16:02:59] ----------------------------------------- +59: +59: [16:02:59] ----------------------------------------- +59: [16:02:59] Finished: testForwardSDSupplier() +59: [16:02:59] ----------------------------------------- +59: +59: [16:02:59] ----------------------------------------- +59: [16:02:59] Finished: testMissingCRSDSupplier() +59: [16:02:59] ----------------------------------------- +59: +59: [16:02:59] ----------------------------------------- +59: [16:02:59] Finished: testIssue3482695() +59: [16:02:59] ----------------------------------------- +59: +59: [16:02:59] ----------------------------------------- +59: [16:02:59] ERROR: Cannot convert 'foo' to unsigned int on line 557 +59: [16:02:59] ERROR: moving to the beginning of the next molecule +59: [16:02:59] Finished: testIssue3525673() +59: [16:02:59] ----------------------------------------- +59: +59: [16:02:59] ----------------------------------------- +59: [16:02:59] Finished: testBlankLinesInProps() +59: [16:02:59] ----------------------------------------- +59: +59: [16:02:59] ----------------------------------------- +59: [16:02:59] Finished: testSkipLines() +59: [16:02:59] ----------------------------------------- +59: +59: [16:02:59] ----------------------------------------- +59: [16:02:59] Finished: testGitHub23() +59: [16:02:59] ----------------------------------------- +59: +59: [16:02:59] ----------------------------------------- +59: [16:02:59] Finished: testGitHub88() +59: [16:02:59] ----------------------------------------- +59: +59: [16:02:59] ----------------------------------------- +59: [16:02:59] Finished: testGitHub2285() +59: [16:02:59] ----------------------------------------- +59: +59: [16:02:59] ----------------------------------------- +59: [16:02:59] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +59: [16:02:59] ERROR: Smiles parse error on line 1 +59: [16:02:59] ERROR: Cannot create molecule from : 'c1ccccc' +59: [16:02:59] SMILES Parse Error: extra open parentheses for input: 'C(C' +59: [16:02:59] ERROR: Smiles parse error on line 3 +59: [16:02:59] ERROR: Cannot create molecule from : 'C(C' +59: [16:02:59] Explicit valence for atom # 1 C, 5, is greater than permitted +59: [16:02:59] ERROR: Could not sanitize molecule on line 5 +59: [16:02:59] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +59: [16:02:59] Explicit valence for atom # 1 F, 2, is greater than permitted +59: [16:02:59] ERROR: Could not sanitize molecule ending on line 21 +59: [16:02:59] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +59: [16:02:59] Explicit valence for atom # 1 F, 2, is greater than permitted +59: [16:02:59] ERROR: Could not sanitize molecule ending on line 21 +59: [16:02:59] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +59: [16:02:59] Explicit valence for atom # 1 F, 2, is greater than permitted +59: [16:02:59] ERROR: Could not sanitize molecule ending on line 21 +59: [16:02:59] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +59: [16:02:59] ERROR: Atom line too short: ' -9.6' on line 28 +59: [16:02:59] ERROR: moving to the beginning of the next molecule +59: [16:02:59] Explicit valence for atom # 1 F, 2, is greater than permitted +59: [16:02:59] ERROR: Could not sanitize molecule ending on line 21 +59: [16:02:59] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +59: [16:02:59] ERROR: Atom line too short: ' -9.6' on line 28 +59: [16:02:59] ERROR: moving to the beginning of the next molecule +59: [16:02:59] Finished: testGitHub2479() +59: [16:02:59] ----------------------------------------- +59: +59: [16:02:59] ----------------------------------------- +59: [16:02:59] +59: +59: **** +59: Invariant Violation +59: bad chiral bond +59: Violation occurred on line 163 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp +59: Failed Expression: bnd +59: **** +59: +59: [16:02:59] Finished: testGitHub2881() +59: [16:02:59] ----------------------------------------- +59: +59: [16:02:59] ----------------------------------------- +59: [16:02:59] Finished: testGitHub3517() +59: [16:02:59] ----------------------------------------- +59: + 53/208 Test #59: testMolSupplier ........................ Passed 0.35 sec test 60 Start 60: testGeneralFileReader 60: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader 60: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 60: Test timeout computed to be: 1500 -55: [19:37:05] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC -55: [19:37:05] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' -55: [19:37:05] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON -55: [19:37:05] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' -60: [19:37:05] +60: [16:02:59] 60: ----------------------------------------- -60: [19:37:05] Finished: testDetermineFormat() -60: [19:37:05] ----------------------------------------- +60: [16:02:59] Finished: testDetermineFormat() +60: [16:02:59] ----------------------------------------- 60: -60: [19:37:05] +60: [16:02:59] 60: ----------------------------------------- -55: [19:37:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -55: [19:37:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged - 45/208 Test #55: smaTest1 ............................... Passed 0.16 sec + 54/208 Test #37: hanoiTest .............................. Passed 4.34 sec test 61 Start 61: testMultithreadedMolSupplier 61: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier 61: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 61: Test timeout computed to be: 1500 -58: *************************************** -58: *************************************** -59: [19:37:05] -59: -59: **** -59: Invariant Violation -59: bad prop value -59: Violation occurred on line 157 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp -59: Failed Expression: nSwaps < 2 -59: **** -59: -61: [19:37:05] -61: ----------------------------------------- -60: [19:37:05] Finished: testSdf() -60: [19:37:05] ----------------------------------------- +60: [16:02:59] Finished: testSdf() +60: [16:02:59] ----------------------------------------- 60: -60: [19:37:05] +60: [16:02:59] 60: ----------------------------------------- -60: [19:37:05] Finished: testSmi() -60: [19:37:05] ----------------------------------------- +61: [16:02:59] +61: ----------------------------------------- +60: [16:02:59] Finished: testSmi() +60: [16:02:59] ----------------------------------------- 60: -60: [19:37:05] +60: [16:02:59] 60: ----------------------------------------- -58: [19:37:05] bond with order 0 found on line 7. This is not part of the MDL specification. -58: [19:37:05] unrecognized query bond type, 9, found on line 7. Using an "any" query. -52: --C1CCC2(CC1)CCCCC2CCC1CCCC1 -58: [19:37:05] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -58: [19:37:05] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -58: [19:37:05] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [19:37:05] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [19:37:05] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [19:37:05] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [19:37:05] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [19:37:05] Warning: molecule is tagged as 3D, but all Z coords are zero -52: smi: ClC1CCCCC1 -52: smi: ClC1CCCCC1 -52: smi: ClC1CCCCC1Br -52: smi: c1ccccc1 -52: smi: c1ccncc1 -52: smi: c1cc[nH]c1 -52: smi: c1cc[nH]c1 -52: smi: c1cc[pH]c1 -58: generating smiles -58: 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 -58: converting back -52: CbC(aC)aC -52: CaC(bC)aC -52: CbC(bC)aC -52: O.C -60: [19:37:05] Finished: testMae() -60: [19:37:05] ----------------------------------------- +60: [16:02:59] Finished: testMae() +60: [16:02:59] ----------------------------------------- 60: -60: [19:37:05] +60: [16:02:59] 60: ----------------------------------------- -60: [19:37:05] Finished: testTdt() -60: [19:37:05] ----------------------------------------- +60: [16:02:59] Finished: testTdt() +60: [16:02:59] ----------------------------------------- 60: -59: [19:37:05] Finished: testMolSup() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -52: 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 - 46/208 Test #60: testGeneralFileReader .................. Passed 0.11 sec + 55/208 Test #60: testGeneralFileReader .................. Passed 0.15 sec test 62 Start 62: testMolWriter 62: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolWriter 62: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 62: Test timeout computed to be: 1500 -52: [19:37:05] SMILES Parse Error: syntax error while parsing: c%()ccccc%() -52: [19:37:05] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' -52: [19:37:05] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) -52: [19:37:05] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' -52: [19:37:05] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' -59: [19:37:05] Finished: testRandMolSup() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -58: check isomorphism -26: ......[19:37:05] Warning: molecule is tagged as 3D, but all Z coords are zero -52: [19:37:05] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' -26: [19:37:05] Molecule does not have explicit Hs. Consider calling AddHs() -52: [19:37:05] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -52: [19:37:05] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -52: [19:37:05] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -52: [19:37:05] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -52: [19:37:05] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -52: [19:37:05] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -52: [19:37:05] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -52: [19:37:05] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -52: [19:37:05] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -52: [19:37:05] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -52: [19:37:05] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -52: [19:37:05] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -52: C=c1s/c2n(c1=O)CCCCCCC\N=2 -52: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 -52: [19:37:05] SMILES Parse Error: extra close parentheses while parsing: C) -52: [19:37:05] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' - 47/208 Test #52: smiTest1 ............................... Passed 0.30 sec +62: [16:02:59] Warning: molecule is tagged as 3D, but all Z coords are zero +62: [16:02:59] Warning: molecule is tagged as 3D, but all Z coords are zero +62: [16:02:59] Warning: molecule is tagged as 3D, but all Z coords are zero +62: [16:02:59] bond with order 0 found on line 11. This is not part of the MDL specification. +62: [16:02:59] bond with order 0 found on line 16. This is not part of the MDL specification. + 56/208 Test #62: testMolWriter .......................... Passed 0.37 sec test 63 Start 63: testTplParser 63: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testTplParser 63: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 63: Test timeout computed to be: 1500 -59: [19:37:05] Finished: testSmilesSup() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] ------------------------------------------------------ -59: [19:37:05] SMILES Parse Error: syntax error while parsing: fail -59: [19:37:05] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -59: [19:37:05] ERROR: Smiles parse error on line 3 -59: [19:37:05] ERROR: Cannot create molecule from : 'fail' -59: [19:37:05] ------------------------------------------------------ -59: [19:37:05] ------------------------------------------------------ -59: [19:37:05] >>> This may result in an infinite loop. It should finish almost immediately: -59: [19:37:05] <<< done. -59: [19:37:05] Finished: testSmilesSupFromText() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] Finished: testSmilesWriter() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -49: [19:37:05] Warning: stereochemistry around double bond may be incorrect in depiction. - 48/208 Test #63: testTplParser .......................... Passed 0.05 sec + 57/208 Test #63: testTplParser .......................... Passed 0.04 sec test 64 Start 64: testMol2ToMol 64: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol 64: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 64: Test timeout computed to be: 1500 -59: [19:37:05] Finished: testSDWriter() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] Finished: testSDSupplierEnding() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] Finished: testSuppliersEmptyFile() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] Finished: testCisTrans() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] Finished: testStereoRound() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] Finished: testIssue226() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] Finished: testTDTSupplier1() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -32: [19:37:05] Maximum BFS search size exceeded. -32: This is likely due to a highly symmetric fused ring system. -59: [19:37:05] Finished: testTDTSupplier2() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] Finished: testTDTSupplier3() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] Finished: testSDSupplierFromText() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] ERROR: Problems encountered parsing data fields -59: [19:37:05] ERROR: moving to the beginning of the next molecule -59: [19:37:05] ERROR: Problems encountered parsing data fields -59: [19:37:05] ERROR: moving to the beginning of the next molecule -59: [19:37:05] Spurious data before the first property will be ignored -59: [19:37:05] Property will be truncated after the first blank line -59: [19:37:05] Property will be truncated after the first blank line -59: [19:37:05] Property will be truncated after the first blank line -59: [19:37:05] Finished: testSDSupplierStrLax1() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] ERROR: Problems encountered parsing data fields -59: [19:37:05] ERROR: moving to the beginning of the next molecule -59: [19:37:05] Property will be truncated after the first blank line -59: [19:37:05] Finished: testSDSupplierStrLax2() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] ERROR: Problems encountered parsing data fields -59: [19:37:05] ERROR: moving to the beginning of the next molecule -59: [19:37:05] ERROR: Problems encountered parsing data fields -59: [19:37:05] ERROR: moving to the beginning of the next molecule -59: [19:37:05] Spurious data before the first property will be ignored -59: [19:37:05] Property will be truncated after the first blank line -59: [19:37:05] Property will be truncated after the first blank line -59: [19:37:05] Property will be truncated after the first blank line -59: [19:37:05] Finished: testSDSupplierFromTextStrLax1() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] ERROR: Problems encountered parsing data fields -59: [19:37:05] ERROR: moving to the beginning of the next molecule -59: [19:37:05] Property will be truncated after the first blank line -59: [19:37:05] Finished: testSDSupplierFromTextStrLax2() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] Finished: testIssue265() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- - 49/208 Test #49: testDepictor ........................... Passed 0.40 sec + 58/208 Test #64: testMol2ToMol .......................... Passed 0.08 sec test 65 Start 65: testSequence 65: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testSequence 65: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 65: Test timeout computed to be: 1500 -59: [19:37:05] ERROR: End of data field name not found -59: [19:37:05] ERROR: moving to the beginning of the next molecule -59: [19:37:05] Explicit valence for atom # 0 F, 2, is greater than permitted -59: [19:37:05] ERROR: Could not sanitize molecule ending on line 16 -59: [19:37:05] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted -59: [19:37:05] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 -59: [19:37:05] ERROR: moving to the beginning of the next molecule -59: [19:37:05] ERROR: Bond line too short: 'M END' on line 18 -59: [19:37:05] ERROR: moving to the beginning of the next molecule -59: [19:37:05] Finished: testSDErrorHandling() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] Finished: testIssue381() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -26: [19:37:05] -26: -26: **** -26: Invariant Violation -26: bad direction in linearSearch -26: Violation occurred on line 240 in file ./Code/Numerics/Optimizer/BFGSOpt.h -26: Failed Expression: status >= 0 -26: **** -26: -59: [19:37:05] Finished: testSetStreamIndices() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] Finished: testMixIterAndRandom() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: build: -59: [19:37:05] Finished: testRemoveHs() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] Finished: testGetItemText() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- - 50/208 Test #64: testMol2ToMol .......................... Passed 0.06 sec -test 66 - Start 66: testExtendedStereoParsing - -66: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing -66: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers -66: Test timeout computed to be: 1500 65: Sequence: GREG 65: HELM: PEPTIDE1{G.R.E.G}$$$$ 65: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O @@ -20372,129 +20675,39 @@ 65: CONECT 27 28 28 29 65: END 65: -59: [19:37:05] Finished: testForwardSDSupplier() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] Finished: testMissingCRSDSupplier() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] Finished: testIssue3482695() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- - 51/208 Test #65: testSequence ........................... Passed 0.05 sec + 59/208 Test #65: testSequence ........................... Passed 0.06 sec +test 66 + Start 66: testExtendedStereoParsing + +66: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing +66: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers +66: Test timeout computed to be: 1500 + 60/208 Test #66: testExtendedStereoParsing .............. Passed 0.03 sec test 67 Start 67: fileParsersCatchTest 67: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 67: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 67: Test timeout computed to be: 1500 -59: [19:37:05] ERROR: Cannot convert 'foo' to unsigned int on line 557 -59: [19:37:05] ERROR: moving to the beginning of the next molecule -59: [19:37:05] Finished: testIssue3525673() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] Finished: testBlankLinesInProps() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] Finished: testSkipLines() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] Finished: testGitHub23() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] Finished: testGitHub88() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] Finished: testGitHub2285() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -59: [19:37:05] ERROR: Smiles parse error on line 1 -59: [19:37:05] ERROR: Cannot create molecule from : 'c1ccccc' - 52/208 Test #66: testExtendedStereoParsing .............. Passed 0.04 sec -test 68 - Start 68: testPropertyLists - -68: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists -68: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers -68: Test timeout computed to be: 1500 -59: [19:37:05] SMILES Parse Error: extra open parentheses for input: 'C(C' -59: [19:37:05] ERROR: Smiles parse error on line 3 -59: [19:37:05] ERROR: Cannot create molecule from : 'C(C' -59: [19:37:05] Explicit valence for atom # 1 C, 5, is greater than permitted -59: [19:37:05] ERROR: Could not sanitize molecule on line 5 -59: [19:37:05] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -59: [19:37:05] Explicit valence for atom # 1 F, 2, is greater than permitted -59: [19:37:05] ERROR: Could not sanitize molecule ending on line 21 -59: [19:37:05] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -59: [19:37:05] Explicit valence for atom # 1 F, 2, is greater than permitted -59: [19:37:05] ERROR: Could not sanitize molecule ending on line 21 -59: [19:37:05] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -59: [19:37:05] Explicit valence for atom # 1 F, 2, is greater than permitted -59: [19:37:05] ERROR: Could not sanitize molecule ending on line 21 -59: [19:37:05] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -59: [19:37:05] ERROR: Atom line too short: ' -9.6' on line 28 -59: [19:37:05] ERROR: moving to the beginning of the next molecule -59: [19:37:05] Explicit valence for atom # 1 F, 2, is greater than permitted -59: [19:37:05] ERROR: Could not sanitize molecule ending on line 21 -59: [19:37:05] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -59: [19:37:05] ERROR: Atom line too short: ' -9.6' on line 28 -59: [19:37:05] ERROR: moving to the beginning of the next molecule -59: [19:37:05] Finished: testGitHub2479() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] -59: -59: **** -59: Invariant Violation -59: bad chiral bond -59: Violation occurred on line 163 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp -59: Failed Expression: bnd -59: **** -59: -59: [19:37:05] Finished: testGitHub2881() -59: [19:37:05] ----------------------------------------- -59: -59: [19:37:05] ----------------------------------------- -59: [19:37:05] Finished: testGitHub3517() -59: [19:37:05] ----------------------------------------- -59: - 53/208 Test #59: testMolSupplier ........................ Passed 0.31 sec -test 69 - Start 69: XYZFileParserCatchTest - -69: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest -69: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers -69: Test timeout computed to be: 1500 -67: [19:37:05] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 -67: [19:37:05] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -67: [19:37:05] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -67: [19:37:05] SGroup 1 is invalid and will be ignored -67: [19:37:05] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -67: [19:37:05] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -67: [19:37:05] SGroup 1 is invalid and will be ignored -67: [19:37:05] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 -67: [19:37:05] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -67: [19:37:05] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -67: [19:37:05] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 -67: [19:37:05] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -67: [19:37:05] SGroup 1 is invalid and will be ignored -67: [19:37:05] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -67: [19:37:05] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -67: [19:37:05] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -67: [19:37:05] SGroup 1 is invalid and will be ignored -67: [19:37:05] SGroup 3 referenced on line 40 not found. -67: [19:37:05] +67: [16:02:59] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 +67: [16:02:59] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +67: [16:02:59] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +67: [16:02:59] SGroup 1 is invalid and will be ignored +67: [16:02:59] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +67: [16:02:59] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +67: [16:02:59] SGroup 1 is invalid and will be ignored +67: [16:02:59] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 +67: [16:02:59] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +67: [16:02:59] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +67: [16:02:59] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 +67: [16:02:59] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +67: [16:02:59] SGroup 1 is invalid and will be ignored +67: [16:02:59] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +67: [16:02:59] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +67: [16:02:59] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +67: [16:02:59] SGroup 1 is invalid and will be ignored +67: [16:02:59] SGroup 3 referenced on line 40 not found. +67: [16:02:59] 67: 67: **** 67: Pre-condition Violation @@ -20503,8 +20716,8 @@ 67: Failed Expression: !d_bonds.empty() 67: **** 67: -67: [19:37:05] SGroup 3 referenced on line 40 not found. -67: [19:37:05] +67: [16:02:59] SGroup 3 referenced on line 40 not found. +67: [16:02:59] 67: 67: **** 67: Pre-condition Violation @@ -20513,13 +20726,13 @@ 67: Failed Expression: !d_bonds.empty() 67: **** 67: -67: [19:37:05] no bonds -67: [19:37:05] SGroup 1 is invalid and will be ignored -67: [19:37:05] SGroup line too short: 'M SBV 1 6' on line 42 -67: [19:37:05] SGroup 1 is invalid and will be ignored -67: [19:37:05] SGroup line too short: 'M SBL 2 3 9 10' on line 46 -67: [19:37:05] SGroup 2 is invalid and will be ignored -67: [19:37:05] +67: [16:02:59] no bonds +67: [16:02:59] SGroup 1 is invalid and will be ignored +67: [16:02:59] SGroup line too short: 'M SBV 1 6' on line 42 +67: [16:02:59] SGroup 1 is invalid and will be ignored +67: [16:02:59] SGroup line too short: 'M SBL 2 3 9 10' on line 46 +67: [16:02:59] SGroup 2 is invalid and will be ignored +67: [16:02:59] 67: 67: **** 67: Pre-condition Violation @@ -20528,7 +20741,7 @@ 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: -67: [19:37:05] +67: [16:02:59] 67: 67: **** 67: Pre-condition Violation @@ -20537,8 +20750,8 @@ 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: -67: [19:37:05] multiple bonds with same bookmark -67: [19:37:05] +67: [16:02:59] multiple bonds with same bookmark +67: [16:02:59] 67: 67: **** 67: Pre-condition Violation @@ -20547,9 +20760,9 @@ 67: Failed Expression: std::find(d_bonds.begin(), d_bonds.end(), bondIdx) != d_bonds.end() 67: **** 67: -67: [19:37:05] bond is not part of the SubstanceGroup -67: [19:37:05] SGroup 2 is invalid and will be ignored -67: [19:37:05] +67: [16:02:59] bond is not part of the SubstanceGroup +67: [16:02:59] SGroup 2 is invalid and will be ignored +67: [16:02:59] 67: 67: **** 67: Pre-condition Violation @@ -20558,7 +20771,7 @@ 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: -67: [19:37:05] +67: [16:02:59] 67: 67: **** 67: Pre-condition Violation @@ -20567,11 +20780,11 @@ 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: -67: [19:37:05] multiple atoms with same bookmark -67: [19:37:05] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. -67: [19:37:05] SGroup 2 is invalid and will be ignored -67: [19:37:05] WARNING: final character of V3000 array is not ')' -67: [19:37:05] +67: [16:02:59] multiple atoms with same bookmark +67: [16:02:59] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. +67: [16:02:59] SGroup 2 is invalid and will be ignored +67: [16:02:59] WARNING: final character of V3000 array is not ')' +67: [16:02:59] 67: 67: **** 67: Pre-condition Violation @@ -20580,8 +20793,8 @@ 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: -67: [19:37:05] WARNING: final character of V3000 array is not ')' -67: [19:37:05] +67: [16:02:59] WARNING: final character of V3000 array is not ')' +67: [16:02:59] 67: 67: **** 67: Pre-condition Violation @@ -20590,10 +20803,10 @@ 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: -67: [19:37:05] multiple bonds with same bookmark -67: [19:37:05] SGroup 1 is invalid and will be ignored -67: [19:37:05] WARNING: final character of V3000 array is not ')' -67: [19:37:05] +67: [16:02:59] multiple bonds with same bookmark +67: [16:02:59] SGroup 1 is invalid and will be ignored +67: [16:02:59] WARNING: final character of V3000 array is not ')' +67: [16:02:59] 67: 67: **** 67: Pre-condition Violation @@ -20602,8 +20815,8 @@ 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: -67: [19:37:05] WARNING: final character of V3000 array is not ')' -67: [19:37:05] +67: [16:02:59] WARNING: final character of V3000 array is not ')' +67: [16:02:59] 67: 67: **** 67: Pre-condition Violation @@ -20612,9 +20825,9 @@ 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: -67: [19:37:05] multiple atoms with same bookmark -67: [19:37:05] SGroup 1 is invalid and will be ignored -67: [19:37:05] +67: [16:02:59] multiple atoms with same bookmark +67: [16:02:59] SGroup 1 is invalid and will be ignored +67: [16:02:59] 67: 67: **** 67: Pre-condition Violation @@ -20623,7 +20836,7 @@ 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: -67: [19:37:05] +67: [16:02:59] 67: 67: **** 67: Pre-condition Violation @@ -20632,9 +20845,9 @@ 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: -67: [19:37:05] multiple bonds with same bookmark -67: [19:37:05] SGroup 2 is invalid and will be ignored -67: [19:37:05] +67: [16:02:59] multiple bonds with same bookmark +67: [16:02:59] SGroup 2 is invalid and will be ignored +67: [16:02:59] 67: 67: **** 67: Pre-condition Violation @@ -20643,7 +20856,7 @@ 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: -67: [19:37:05] +67: [16:02:59] 67: 67: **** 67: Pre-condition Violation @@ -20652,118 +20865,14 @@ 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: -67: [19:37:05] multiple atoms with same bookmark -67: [19:37:05] SGroup 2 is invalid and will be ignored -51: ....E..... -51: ====================================================================== -51: ERROR: test5SamplingMimic3D (__main__.TestCase.test5SamplingMimic3D) -51: ---------------------------------------------------------------------- -51: Traceback (most recent call last): -51: File "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/testDepictor.py", line 188, in test5SamplingMimic3D -51: dmat3D = getDistMat(mol) -51: ^^^^^^^^^^^^^^^ -51: File "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/testDepictor.py", line 31, in getDistMat -51: res = np.zeros(nl, np.float) -51: ^^^^^^^^ -51: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ -51: raise AttributeError(__former_attrs__[attr]) -51: AttributeError: module 'numpy' has no attribute 'float'. -51: `np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here. -51: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: -51: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations -51: -51: ---------------------------------------------------------------------- -51: Ran 10 tests in 0.254s -51: -51: FAILED (errors=1) -67: [19:37:05] Explicit valence for atom # 2 O, 3, is greater than permitted -67: [19:37:05] Explicit valence for atom # 1 O, 3, is greater than permitted -67: [19:37:05] Explicit valence for atom # 1 C, 5, is greater than permitted -69: =============================================================================== -69: All tests passed (100 assertions in 2 test cases) -69: - 54/208 Test #69: XYZFileParserCatchTest ................. Passed 0.03 sec -test 70 - Start 70: cdxmlParserCatchTest - -70: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest -70: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers -70: Test timeout computed to be: 1500 -68: =============================================================================== -68: All tests passed (94 assertions in 4 test cases) -68: - 55/208 Test #68: testPropertyLists ...................... Passed 0.04 sec -test 71 - Start 71: testSubstructMatch - -71: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -71: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct -71: Test timeout computed to be: 1500 -67: [19:37:05] sanitise [19:37:05] UNK: [19:37:05] Warning: molecule is tagged as 3D, but all Z coords are zero -26: ... - 56/208 Test #51: pyDepictor .............................***Failed 0.52 sec -....E..... -====================================================================== -ERROR: test5SamplingMimic3D (__main__.TestCase.test5SamplingMimic3D) ----------------------------------------------------------------------- -Traceback (most recent call last): - File "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/testDepictor.py", line 188, in test5SamplingMimic3D - dmat3D = getDistMat(mol) - ^^^^^^^^^^^^^^^ - File "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/testDepictor.py", line 31, in getDistMat - res = np.zeros(nl, np.float) - ^^^^^^^^ - File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ - raise AttributeError(__former_attrs__[attr]) -AttributeError: module 'numpy' has no attribute 'float'. -`np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here. -The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: - https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations - ----------------------------------------------------------------------- -Ran 10 tests in 0.254s - -FAILED (errors=1) - -test 72 - Start 72: substructTestCatch - -72: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct/substructTestCatch -72: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct -72: Test timeout computed to be: 1500 -26: ---------------------------------------------------------------------- -26: Ran 12 tests in 0.625s -26: -26: OK -71: ----------------- Test 1 -71: Done -71: -71: ----------------- Test 2 -71: Done -71: -71: ----------------- Test 3 -71: Done -71: -71: ----------------- Test 4 -71: Done -71: -71: ----------------- Test 5 -71: Done -71: -71: ----------------- Test 5 QueryRoot -71: Done -71: -71: ----------------- Test 6 (Issue71 related) -71: Done -71: -71: ----------------- Testing serial numbers on recursive queries -71: Done -71: -71: [19:37:06] ------------------------------------- -71: [19:37:06] Test multithreading -71: reading molecules -67: [19:37:06] skipping block at line 7: 'BEGIN ATOM' -67: [19:37:06] +67: [16:02:59] multiple atoms with same bookmark +67: [16:02:59] SGroup 2 is invalid and will be ignored +67: [16:02:59] Explicit valence for atom # 2 O, 3, is greater than permitted +67: [16:02:59] Explicit valence for atom # 1 O, 3, is greater than permitted +67: [16:02:59] Explicit valence for atom # 1 C, 5, is greater than permitted +67: [16:02:59] sanitise [16:02:59] UNK: [16:02:59] Warning: molecule is tagged as 3D, but all Z coords are zero +67: [16:02:59] skipping block at line 7: 'BEGIN ATOM' +67: [16:02:59] 67: 67: **** 67: Pre-condition Violation @@ -20772,7 +20881,7 @@ 67: Failed Expression: dp_inStream 67: **** 67: -67: [19:37:06] +67: [16:02:59] 67: 67: **** 67: Pre-condition Violation @@ -20781,7 +20890,7 @@ 67: Failed Expression: dp_inStream 67: **** 67: -67: [19:37:06] +67: [16:02:59] 67: 67: **** 67: Pre-condition Violation @@ -20790,7 +20899,7 @@ 67: Failed Expression: dp_inStream 67: **** 67: -67: [19:37:06] +67: [16:02:59] 67: 67: **** 67: Pre-condition Violation @@ -20799,7 +20908,7 @@ 67: Failed Expression: dp_inStream 67: **** 67: -67: [19:37:06] +67: [16:02:59] 67: 67: **** 67: Pre-condition Violation @@ -20808,9 +20917,9 @@ 67: Failed Expression: dp_sInStream != nullptr 67: **** 67: -67: [19:37:06] Found a SCD/SED line with missing/empty SDT specification at line 21 -67: [19:37:06] Found a SCD/SED line with missing/empty SDT specification at line 20 -67: [19:37:06] +67: [16:02:59] Found a SCD/SED line with missing/empty SDT specification at line 21 +67: [16:02:59] Found a SCD/SED line with missing/empty SDT specification at line 20 +67: [16:02:59] 67: 67: **** 67: Post-condition Violation @@ -20819,13 +20928,13 @@ 67: Failed Expression: anum > -1 67: **** 67: -67: [19:37:06] BEGIN SGROUP line not found on line 14 -67: [19:37:06] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. -67: [19:37:06] END SGROUP line not found on line 14 -67: [19:37:06] END SGROUP line not found on line 14 -67: [19:37:06] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. -67: [19:37:06] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. -67: [19:37:06] +67: [16:02:59] BEGIN SGROUP line not found on line 14 +67: [16:02:59] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. +67: [16:02:59] END SGROUP line not found on line 14 +67: [16:02:59] END SGROUP line not found on line 14 +67: [16:02:59] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. +67: [16:02:59] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. +67: [16:02:59] 67: 67: **** 67: Range Error @@ -20834,281 +20943,118 @@ 67: Failed Expression: 99 < 9 67: **** 67: -67: [19:37:06] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. -67: [19:37:06] Multiple ATTCHPT values for atom 2 on line 9 -67: [19:37:06] Found a SCD/SED line with missing/empty SDT specification at line 12 -67: [19:37:06] SMARTS Parse Error: syntax error while parsing: [#6;R -67: [19:37:06] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' -67: [19:37:06] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. -67: [19:37:06] Skipping empty SMARTS value for SMARTSQ. -67: [19:37:06] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. -67: [19:37:06] Found a SCD/SED line with missing/empty SDT specification at line 12 -67: [19:37:06] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -67: [19:37:06] Warning: molecule is tagged as 3D, but all Z coords are zero +67: [16:02:59] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. +67: [16:02:59] Multiple ATTCHPT values for atom 2 on line 9 +67: [16:02:59] Found a SCD/SED line with missing/empty SDT specification at line 12 +67: [16:02:59] SMARTS Parse Error: syntax error while parsing: [#6;R +67: [16:02:59] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' +67: [16:02:59] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. +67: [16:02:59] Skipping empty SMARTS value for SMARTSQ. +67: [16:02:59] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. +67: [16:02:59] Found a SCD/SED line with missing/empty SDT specification at line 12 +67: [16:02:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +67: [16:02:59] Warning: molecule is tagged as 3D, but all Z coords are zero 67: =============================================================================== 67: All tests passed (778 assertions in 67 test cases) 67: - 57/208 Test #67: fileParsersCatchTest ................... Passed 0.12 sec -test 73 - Start 73: testGenericGroups + 61/208 Test #67: fileParsersCatchTest ................... Passed 0.14 sec +test 68 + Start 68: testPropertyLists -73: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups -73: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups -73: Test timeout computed to be: 1500 -70: [19:37:06] Invalid or missing fragment id from CDXML fragment, assigning new one... -70: [19:37:06] Explicit valence for atom # 3 N, 4, is greater than permitted -70: [19:37:06] CDXMLParser: failed sanitizing skipping fragment 32 -70: [19:37:06] Bad bond in CDXML skipping fragment 58... -70: [19:37:06] Invalid or missing fragment id from CDXML fragment, assigning new one... -70: [19:37:06] Bad bond in CDXML skipping fragment 58... - 58/208 Test #26: pyForceFieldConstraints ................ Passed 0.95 sec -test 74 - Start 74: testReaction +68: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists +68: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers +68: Test timeout computed to be: 1500 +68: =============================================================================== +68: All tests passed (94 assertions in 4 test cases) +68: + 62/208 Test #68: testPropertyLists ...................... Passed 0.03 sec +test 69 + Start 69: XYZFileParserCatchTest -74: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testReaction -74: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions -74: Test timeout computed to be: 1500 +69: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest +69: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers +69: Test timeout computed to be: 1500 +69: =============================================================================== +69: All tests passed (100 assertions in 2 test cases) +69: + 63/208 Test #69: XYZFileParserCatchTest ................. Passed 0.04 sec +test 70 + Start 70: cdxmlParserCatchTest + +70: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest +70: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers +70: Test timeout computed to be: 1500 +70: [16:03:00] Invalid or missing fragment id from CDXML fragment, assigning new one... +70: [16:03:00] Explicit valence for atom # 3 N, 4, is greater than permitted +70: [16:03:00] CDXMLParser: failed sanitizing skipping fragment 32 +70: [16:03:00] Bad bond in CDXML skipping fragment 58... +70: [16:03:00] Invalid or missing fragment id from CDXML fragment, assigning new one... +70: [16:03:00] Bad bond in CDXML skipping fragment 58... +70: [16:03:00] WARNING: not removing hydrogen atom without neighbors +70: [16:03:00] WARNING: not removing hydrogen atom without neighbors +70: [16:03:00] WARNING: not removing hydrogen atom without neighbors +70: [16:03:00] WARNING: not removing hydrogen atom without neighbors +70: [16:03:00] WARNING: not removing hydrogen atom without neighbors +70: [16:03:00] WARNING: not removing hydrogen atom without neighbors +70: [16:03:00] WARNING: not removing hydrogen atom without neighbors +70: [16:03:00] WARNING: not removing hydrogen atom without neighbors +70: [16:03:00] WARNING: not removing hydrogen atom without neighbors +70: [16:03:00] WARNING: not removing hydrogen atom without neighbors +70: [16:03:00] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents fragment 64603 not found in document. +70: [16:03:00] Incomplete atom labelling, cannot make bond +70: [16:03:00] Incomplete atom labelling, cannot make bond +70: [16:03:00] Incomplete atom labelling, cannot make bond +70: [16:03:00] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +70: [16:03:00] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +70: [16:03:00] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +70: [16:03:00] Failed to parse XML fragment 5 node: b attribute: Order: 5 +70: [16:03:00] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +70: [16:03:00] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +70: [16:03:00] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +70: [16:03:00] Failed to parse XML fragment 5 node: b attribute: Order: 5 +70: =============================================================================== +70: All tests passed (200 assertions in 1 test case) +70: + 64/208 Test #70: cdxmlParserCatchTest ................... Passed 0.18 sec +test 71 + Start 71: testSubstructMatch + +71: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +71: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct +71: Test timeout computed to be: 1500 +71: ----------------- Test 1 +71: Done +71: +71: ----------------- Test 2 +71: Done +71: +71: ----------------- Test 3 +71: Done +71: +71: ----------------- Test 4 +71: Done +71: +71: ----------------- Test 5 +71: Done +71: +71: ----------------- Test 5 QueryRoot +71: Done +71: +71: ----------------- Test 6 (Issue71 related) +71: Done +71: +71: ----------------- Testing serial numbers on recursive queries +71: Done +71: +71: [16:03:00] ------------------------------------- +71: [16:03:00] Test multithreading +71: reading molecules 71: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 71: processing 71: launch :0 71: launch :1 71: launch :2 71: launch :3 -62: [19:37:06] Warning: molecule is tagged as 3D, but all Z coords are zero -62: [19:37:06] Warning: molecule is tagged as 3D, but all Z coords are zero -62: [19:37:06] Warning: molecule is tagged as 3D, but all Z coords are zero -62: [19:37:06] bond with order 0 found on line 11. This is not part of the MDL specification. -62: [19:37:06] bond with order 0 found on line 16. This is not part of the MDL specification. -70: [19:37:06] WARNING: not removing hydrogen atom without neighbors -70: [19:37:06] WARNING: not removing hydrogen atom without neighbors -70: [19:37:06] WARNING: not removing hydrogen atom without neighbors -70: [19:37:06] WARNING: not removing hydrogen atom without neighbors -70: [19:37:06] WARNING: not removing hydrogen atom without neighbors -70: [19:37:06] WARNING: not removing hydrogen atom without neighbors -70: [19:37:06] WARNING: not removing hydrogen atom without neighbors -70: [19:37:06] WARNING: not removing hydrogen atom without neighbors -73: =============================================================================== -73: All tests passed (490 assertions in 18 test cases) -73: - 59/208 Test #73: testGenericGroups ...................... Passed 0.08 sec -test 75 - Start 75: testReactionFingerprints - -75: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints -75: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions -75: Test timeout computed to be: 1500 -70: [19:37:06] WARNING: not removing hydrogen atom without neighbors -70: [19:37:06] WARNING: not removing hydrogen atom without neighbors -70: [19:37:06] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents fragment 64603 not found in document. - 60/208 Test #62: testMolWriter .......................... Passed 0.35 sec -test 76 - Start 76: testEnumeration - -76: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration -76: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions -76: Test timeout computed to be: 1500 -74: smi: O=C1CNC(=O)CN1 -74: 1: O=C1CNC(=O)CN1 -74: 2: COOC -74: [19:37:06] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -74: [19:37:06] 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]' -74: O=C1CNC(=O)CN1 -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: [19:37:06] mapped atoms in the reactants were not mapped in the products. -74: unmapped numbers are: 4 -75: [19:37:06] ------------------------------------- -75: [19:37:06] Test Reaction StructuralFingerprint -74: [19:37:06] atom 0 in product 0 has multiple charge specifications. -74: mass: 15.0001 -74: Oc1ccccn1 -74: Oc1ccc[nH]1 -70: [19:37:06] Incomplete atom labelling, cannot make bond -70: [19:37:06] Incomplete atom labelling, cannot make bond -70: [19:37:06] Incomplete atom labelling, cannot make bond -75: [19:37:06] ------------------------------------- -75: [19:37:06] Test Reaction DifferenceFingerprint -74: [19:37:06] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] -74: [19:37:06] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' -74: [19:37:06] SMARTS Parse Error: syntax error while parsing: ([C:2] -74: [19:37:06] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -74: [19:37:06] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] -74: [19:37:06] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' -74: [19:37:06] SMARTS Parse Error: syntax error while parsing: [C:2]) -74: [19:37:06] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' - 61/208 Test #75: testReactionFingerprints ............... Passed 0.05 sec -test 77 - Start 77: rxnTestCatch - -77: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch -77: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions -77: Test timeout computed to be: 1500 -70: [19:37:06] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -70: [19:37:06] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -70: [19:37:06] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -70: [19:37:06] Failed to parse XML fragment 5 node: b attribute: Order: 5 -74: [19:37:06] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -74: [19:37:06] 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]' -74: [19:37:06] reactant 2 has no mapped atoms. -74: [19:37:06] >> Atoms within one molecule have different RXN roles. -74: [19:37:06] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. -74: [19:37:06] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] -74: [19:37:06] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' -74: [19:37:06] SMARTS Parse Error: syntax error while parsing: ([C:2] -74: [19:37:06] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -74: [19:37:06] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) -74: [19:37:06] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' -74: [19:37:06] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] -74: [19:37:06] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' -74: [19:37:06] reactant 0 has no mapped atoms. -74: [19:37:06] reactant 1 has no mapped atoms. -74: [19:37:06] reactant 3 has no mapped atoms. -74: [19:37:06] product atom-mapping number 2 found multiple times. -74: [19:37:06] product atom-mapping number 3 found multiple times. -74: [19:37:06] product atom-mapping number 4 found multiple times. -74: [19:37:06] product atom-mapping number 5 found multiple times. -74: [19:37:06] product atom-mapping number 6 found multiple times. -74: [19:37:06] product atom-mapping number 7 found multiple times. -74: [19:37:06] product atom-mapping number 8 found multiple times. -74: [19:37:06] product atom-mapping number 12 found multiple times. -74: [19:37:06] product atom-mapping number 9 found multiple times. -74: [19:37:06] product atom-mapping number 10 found multiple times. -74: [19:37:06] product atom-mapping number 11 found multiple times. -74: [19:37:06] reactant 0 has no mapped atoms. -74: [19:37:06] reactant 1 has no mapped atoms. -74: [19:37:06] reactant 3 has no mapped atoms. -74: [19:37:06] reactant atom-mapping number 19 found multiple times. -74: [19:37:06] reactant atom-mapping number 25 found multiple times. -74: [19:37:06] reactant atom-mapping number 20 found multiple times. -74: [19:37:06] reactant atom-mapping number 21 found multiple times. -74: [19:37:06] reactant atom-mapping number 22 found multiple times. -74: [19:37:06] reactant atom-mapping number 23 found multiple times. -74: [19:37:06] reactant atom-mapping number 24 found multiple times. -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: [19:37:06] product atom-mapping number 2 found multiple times. -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: [19:37:06] product atom-mapping number 2 found multiple times. -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: [19:37:06] product atom-mapping number 2 found multiple times. -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: [19:37:06] product atom-mapping number 2 found multiple times. -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -70: [19:37:06] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -70: [19:37:06] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -70: [19:37:06] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -70: [19:37:06] Failed to parse XML fragment 5 node: b attribute: Order: 5 -70: =============================================================================== -70: All tests passed (200 assertions in 1 test case) -70: -74: [19:37:06] product atom-mapping number 2 found multiple times. -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: [19:37:06] product atom-mapping number 2 found multiple times. -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -74: [19:37:06] product atom-mapping number 5 found multiple times. -74: [19:37:06] product atom-mapping number 2 found multiple times. -74: [19:37:06] product atom-mapping number 3 found multiple times. -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: [19:37:06] product atom-mapping number 4 found multiple times. -74: [19:37:06] product atom-mapping number 5 found multiple times. -74: [19:37:06] product atom-mapping number 2 found multiple times. -74: [19:37:06] product atom-mapping number 3 found multiple times. -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: [19:37:06] product atom-mapping number 4 found multiple times. - 62/208 Test #70: cdxmlParserCatchTest ................... Passed 0.19 sec -test 78 - Start 78: pyChemReactions - -78: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" -78: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap -78: Test timeout computed to be: 1500 -74: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -74: [19:37:06] product atom-mapping number 5 found multiple times. -74: [19:37:06] product atom-mapping number 2 found multiple times. -74: [19:37:06] product atom-mapping number 3 found multiple times. -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: [19:37:06] product atom-mapping number 4 found multiple times. -74: [19:37:06] product atom-mapping number 5 found multiple times. -74: [19:37:06] product atom-mapping number 2 found multiple times. -74: [19:37:06] product atom-mapping number 3 found multiple times. -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: [19:37:06] product atom-mapping number 4 found multiple times. -74: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -74: [19:37:06] product atom-mapping number 2 found multiple times. -74: [19:37:06] product atom-mapping number 3 found multiple times. -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: [19:37:06] product atom-mapping number 4 found multiple times. -74: [19:37:06] product atom-mapping number 2 found multiple times. -74: [19:37:06] product atom-mapping number 3 found multiple times. -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: [19:37:06] product atom-mapping number 4 found multiple times. -74: F[C@@](Cl)(Br)O[C@](F)(Cl)Br -74: [19:37:06] product atom-mapping number 2 found multiple times. -74: [19:37:06] product atom-mapping number 3 found multiple times. -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: [19:37:06] product atom-mapping number 4 found multiple times. -74: [19:37:06] product atom-mapping number 2 found multiple times. -74: [19:37:06] product atom-mapping number 3 found multiple times. -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: [19:37:06] product atom-mapping number 4 found multiple times. -74: F[C@](Cl)(Br)O[C@](F)(Cl)Br -74: [19:37:06] product atom-mapping number 4 found multiple times. -74: [19:37:06] product atom-mapping number 3 found multiple times. -74: [19:37:06] product atom-mapping number 2 found multiple times. -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: [19:37:06] product atom-mapping number 4 found multiple times. -74: [19:37:06] product atom-mapping number 3 found multiple times. -74: [19:37:06] product atom-mapping number 2 found multiple times. -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: [19:37:06] product atom-mapping number 4 found multiple times. -74: [19:37:06] product atom-mapping number 3 found multiple times. -74: [19:37:06] product atom-mapping number 2 found multiple times. -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: [19:37:06] product atom-mapping number 4 found multiple times. -74: [19:37:06] product atom-mapping number 3 found multiple times. -74: [19:37:06] product atom-mapping number 2 found multiple times. -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: [19:37:06] product atom-mapping number 3 found multiple times. -74: [19:37:06] product atom-mapping number 2 found multiple times. -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: [19:37:06] mapped atoms in the reactants were not mapped in the products. -74: unmapped numbers are: 4 -74: [19:37:06] product atom-mapping number 3 found multiple times. -74: [19:37:06] product atom-mapping number 2 found multiple times. -74: [19:37:06] product atom-mapping number 1 found multiple times. -74: [19:37:06] mapped atoms in the reactants were not mapped in the products. -74: unmapped numbers are: 4 -74: [19:37:06] product atom-mapping number 6 not found in reactants. -74: [19:37:06] product atom-mapping number 7 not found in reactants. -74: [19:37:06] product atom-mapping number 8 not found in reactants. -74: [19:37:06] product atom-mapping number 7 not found in reactants. -74: [19:37:06] product atom-mapping number 8 not found in reactants. -74: [19:37:06] product atom-mapping number 9 not found in reactants. -74: [19:37:06] product atom-mapping number 10 not found in reactants. -74: [19:37:06] mapped atoms in the reactants were not mapped in the products. -74: unmapped numbers are: 6 -74: [19:37:06] product atom-mapping number 7 not found in reactants. -74: [19:37:06] product atom-mapping number 8 not found in reactants. -74: [19:37:06] product atom-mapping number 9 not found in reactants. -74: [19:37:06] product atom-mapping number 10 not found in reactants. -74: [19:37:06] mapped atoms in the reactants were not mapped in the products. -74: unmapped numbers are: 6 -74: 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] -74: smi2 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] -74: [19:37:06] mapped atoms in the reactants were not mapped in the products. -74: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 -77: [19:37:06] atom 0 in product 0 has multiple charge specifications. -77: [19:37:06] mapped atoms in the reactants were not mapped in the products. -77: unmapped numbers are: 2 -77: [19:37:06] mapped atoms in the reactants were not mapped in the products. -77: unmapped numbers are: 2 -77: [19:37:06] SMARTS Parse Error: unclosed ring for input: 'CC1' -77: [19:37:06] SMILES Parse Error: unclosed ring for input: 'CC1' -77: [19:37:06] mapped atoms in the reactants were not mapped in the products. -77: unmapped numbers are: 2 71: done 71: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 71: processing2 @@ -21116,25 +21062,6 @@ 71: launch2 :1 71: launch2 :2 71: launch2 :3 -74: [19:37:06] product atom-mapping number 17 not found in reactants. -74: [19:37:06] product atom-mapping number 18 not found in reactants. -74: [19:37:06] mapped atoms in the reactants were not mapped in the products. -74: unmapped numbers are: 12 -77: [19:37:06] product atom-mapping number 2 not found in reactants. -77: [19:37:06] mapped atoms in the reactants were not mapped in the products. -77: unmapped numbers are: 2 -77: [19:37:06] product atom-mapping number 2 not found in reactants. -77: [19:37:06] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -77: =============================================================================== -77: All tests passed (450 assertions in 14 test cases) -77: - 63/208 Test #77: rxnTestCatch ........................... Passed 0.12 sec -test 79 - Start 79: pyChemReactionEnumerations - -79: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" -79: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap -79: Test timeout computed to be: 1500 71: done 71: preprocessing 3 71: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 @@ -21143,74 +21070,42 @@ 71: launch3 :1 71: launch3 :2 71: launch3 :3 -72: =============================================================================== -72: All tests passed (91 assertions in 5 test cases) -72: - 64/208 Test #72: substructTestCatch ..................... Passed 0.30 sec -test 80 - Start 80: pyChemReactionSanitize - -80: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" -80: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap -80: Test timeout computed to be: 1500 -76: 30000000 30000000 -74: [19:37:06] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -74: [19:37:06] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -74: -74: [19:37:06] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels -32: [19:37:06] Maximum BFS search size exceeded. -32: This is likely due to a highly symmetric fused ring system. -74: ------------- -74: CCOc1ccccc1 -32: F/C=C/Cl -32: [H]/C(F)=C(/[H])Cl -32: F/C=C/Cl -32: F/C=C/Cl -32: C/C(F)=C(/C)Cl - 65/208 Test #32: graphmolMolOpsTest ..................... Passed 1.22 sec -test 81 - Start 81: testChemTransforms + 65/208 Test #39: resMolSupplierTest ..................... Passed 5.77 sec +test 72 + Start 72: substructTestCatch -81: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms -81: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms -81: Test timeout computed to be: 1500 -81: 1 smi: CC -81: 1 smi: CC -81: 2 smi: CCO[C@H](N)P -81: 2 smi: CC -81: replaceSub smi1:CCP(CC)[C@@H](N)O -81: replaceSub smi1:CCNCC -81: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O -81: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O +72: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct/substructTestCatch +72: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Substruct +72: Test timeout computed to be: 1500 71: done -71: [19:37:06] done -71: [19:37:06] ------------------------------------- -71: [19:37:06] Test GitHub issue 15 -71: [19:37:06] done -71: [19:37:06] ------------------------------------- -71: [19:37:06] Test GitHub issue 409 -71: [19:37:06] done -71: [19:37:06] ------------------------------------- -71: [19:37:06] Test chiral matching -71: [19:37:06] done -71: [19:37:06] ------------------------------------- -71: [19:37:06] Test GitHub issue 688: partially specified chiral substructure queries don't work properly -71: [19:37:06] done -71: [19:37:06] ------------------------------------- -71: [19:37:06] Test dative-bond matching -71: [19:37:06] done -71: [19:37:06] ------------------------------------- -71: [19:37:06] Test cis/trans matching -71: [19:37:06] done -71: [19:37:06] ------------------------------------- -71: [19:37:06] Test cis/trans matching part 2 -71: [19:37:06] done -71: [19:37:06] ------------------------------------- -71: [19:37:06] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS -71: [19:37:06] done -71: [19:37:06] ------------------------------------- -71: [19:37:06] Testing matching E/Z against Cis/Trans stereo bonds -71: [19:37:06] +71: [16:03:00] done +71: [16:03:00] ------------------------------------- +71: [16:03:00] Test GitHub issue 15 +71: [16:03:00] done +71: [16:03:00] ------------------------------------- +71: [16:03:00] Test GitHub issue 409 +71: [16:03:00] done +71: [16:03:00] ------------------------------------- +71: [16:03:00] Test chiral matching +71: [16:03:00] done +71: [16:03:00] ------------------------------------- +71: [16:03:00] Test GitHub issue 688: partially specified chiral substructure queries don't work properly +71: [16:03:00] done +71: [16:03:00] ------------------------------------- +71: [16:03:00] Test dative-bond matching +71: [16:03:00] done +71: [16:03:00] ------------------------------------- +71: [16:03:00] Test cis/trans matching +71: [16:03:00] done +71: [16:03:00] ------------------------------------- +71: [16:03:00] Test cis/trans matching part 2 +71: [16:03:00] done +71: [16:03:00] ------------------------------------- +71: [16:03:00] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS +71: [16:03:00] done +71: [16:03:00] ------------------------------------- +71: [16:03:00] Testing matching E/Z against Cis/Trans stereo bonds +71: [16:03:00] 71: 71: **** 71: Pre-condition Violation @@ -21219,7 +21114,7 @@ 71: Failed Expression: !matches.empty() 71: **** 71: -71: [19:37:06] +71: [16:03:00] 71: 71: **** 71: Pre-condition Violation @@ -21228,16 +21123,293 @@ 71: Failed Expression: !matches.empty() 71: **** 71: - 66/208 Test #71: testSubstructMatch ..................... Passed 0.47 sec -test 82 - Start 82: chemTransformsTestCatch + 66/208 Test #71: testSubstructMatch ..................... Passed 0.49 sec +test 73 + Start 73: testGenericGroups -82: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -82: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms -82: Test timeout computed to be: 1500 -81: [19:37:06] SMARTS Parse Error: syntax error while parsing: bar -81: [19:37:06] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' -78: [19:37:06] +73: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups +73: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups +73: Test timeout computed to be: 1500 +73: =============================================================================== +73: All tests passed (490 assertions in 18 test cases) +73: + 67/208 Test #73: testGenericGroups ...................... Passed 0.06 sec +test 74 + Start 74: testReaction + +74: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testReaction +74: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions +74: Test timeout computed to be: 1500 +74: smi: O=C1CNC(=O)CN1 +74: 1: O=C1CNC(=O)CN1 +74: 2: COOC +74: [16:03:00] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +74: [16:03:00] SMARTS Parse Error: Failed parsing SMARTS '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' +74: O=C1CNC(=O)CN1 +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: [16:03:00] mapped atoms in the reactants were not mapped in the products. +74: unmapped numbers are: 4 +74: [16:03:00] atom 0 in product 0 has multiple charge specifications. +74: mass: 15.0001 +72: =============================================================================== +72: All tests passed (91 assertions in 5 test cases) +72: +74: Oc1ccccn1 +74: Oc1ccc[nH]1 + 68/208 Test #72: substructTestCatch ..................... Passed 0.34 sec +test 75 + Start 75: testReactionFingerprints + +75: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints +75: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions +75: Test timeout computed to be: 1500 +74: [16:03:00] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] +74: [16:03:00] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' +74: [16:03:00] SMARTS Parse Error: syntax error while parsing: ([C:2] +74: [16:03:00] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +74: [16:03:00] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] +74: [16:03:00] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' +74: [16:03:00] SMARTS Parse Error: syntax error while parsing: [C:2]) +74: [16:03:00] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' +74: [16:03:00] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +74: [16:03:00] SMILES Parse Error: Failed parsing SMILES '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' +74: [16:03:00] reactant 2 has no mapped atoms. +75: [16:03:00] ------------------------------------- +75: [16:03:00] Test Reaction StructuralFingerprint +74: [16:03:00] >> Atoms within one molecule have different RXN roles. +74: [16:03:00] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. +74: [16:03:00] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] +74: [16:03:00] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' +74: [16:03:00] SMARTS Parse Error: syntax error while parsing: ([C:2] +74: [16:03:00] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +74: [16:03:00] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) +74: [16:03:00] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' +74: [16:03:00] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] +74: [16:03:00] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' +74: [16:03:00] reactant 0 has no mapped atoms. +74: [16:03:00] reactant 1 has no mapped atoms. +74: [16:03:00] reactant 3 has no mapped atoms. +74: [16:03:00] product atom-mapping number 2 found multiple times. +74: [16:03:00] product atom-mapping number 3 found multiple times. +74: [16:03:00] product atom-mapping number 4 found multiple times. +74: [16:03:00] product atom-mapping number 5 found multiple times. +74: [16:03:00] product atom-mapping number 6 found multiple times. +74: [16:03:00] product atom-mapping number 7 found multiple times. +74: [16:03:00] product atom-mapping number 8 found multiple times. +74: [16:03:00] product atom-mapping number 12 found multiple times. +74: [16:03:00] product atom-mapping number 9 found multiple times. +74: [16:03:00] product atom-mapping number 10 found multiple times. +74: [16:03:00] product atom-mapping number 11 found multiple times. +74: [16:03:00] reactant 0 has no mapped atoms. +74: [16:03:00] reactant 1 has no mapped atoms. +74: [16:03:00] reactant 3 has no mapped atoms. +74: [16:03:00] reactant atom-mapping number 19 found multiple times. +74: [16:03:00] reactant atom-mapping number 25 found multiple times. +74: [16:03:00] reactant atom-mapping number 20 found multiple times. +74: [16:03:00] reactant atom-mapping number 21 found multiple times. +74: [16:03:00] reactant atom-mapping number 22 found multiple times. +74: [16:03:00] reactant atom-mapping number 23 found multiple times. +74: [16:03:00] reactant atom-mapping number 24 found multiple times. +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: [16:03:00] product atom-mapping number 2 found multiple times. +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: [16:03:00] product atom-mapping number 2 found multiple times. +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: [16:03:00] product atom-mapping number 2 found multiple times. +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: [16:03:00] product atom-mapping number 2 found multiple times. +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br +74: [16:03:00] product atom-mapping number 2 found multiple times. +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: [16:03:00] product atom-mapping number 2 found multiple times. +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br +74: [16:03:00] product atom-mapping number 5 found multiple times. +74: [16:03:00] product atom-mapping number 2 found multiple times. +74: [16:03:00] product atom-mapping number 3 found multiple times. +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: [16:03:00] product atom-mapping number 4 found multiple times. +74: [16:03:00] product atom-mapping number 5 found multiple times. +74: [16:03:00] product atom-mapping number 2 found multiple times. +74: [16:03:00] product atom-mapping number 3 found multiple times. +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: [16:03:00] product atom-mapping number 4 found multiple times. +74: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br +74: [16:03:00] product atom-mapping number 5 found multiple times. +74: [16:03:00] product atom-mapping number 2 found multiple times. +74: [16:03:00] product atom-mapping number 3 found multiple times. +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: [16:03:00] product atom-mapping number 4 found multiple times. +74: [16:03:00] product atom-mapping number 5 found multiple times. +74: [16:03:00] product atom-mapping number 2 found multiple times. +74: [16:03:00] product atom-mapping number 3 found multiple times. +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: [16:03:00] product atom-mapping number 4 found multiple times. +74: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br +74: [16:03:00] product atom-mapping number 2 found multiple times. +74: [16:03:00] product atom-mapping number 3 found multiple times. +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: [16:03:00] product atom-mapping number 4 found multiple times. +74: [16:03:00] product atom-mapping number 2 found multiple times. +74: [16:03:00] product atom-mapping number 3 found multiple times. +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: [16:03:00] product atom-mapping number 4 found multiple times. +74: F[C@@](Cl)(Br)O[C@](F)(Cl)Br +74: [16:03:00] product atom-mapping number 2 found multiple times. +74: [16:03:00] product atom-mapping number 3 found multiple times. +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: [16:03:00] product atom-mapping number 4 found multiple times. +74: [16:03:00] product atom-mapping number 2 found multiple times. +74: [16:03:00] product atom-mapping number 3 found multiple times. +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: [16:03:00] product atom-mapping number 4 found multiple times. +74: F[C@](Cl)(Br)O[C@](F)(Cl)Br +74: [16:03:00] product atom-mapping number 4 found multiple times. +74: [16:03:00] product atom-mapping number 3 found multiple times. +74: [16:03:00] product atom-mapping number 2 found multiple times. +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: [16:03:00] product atom-mapping number 4 found multiple times. +74: [16:03:00] product atom-mapping number 3 found multiple times. +74: [16:03:00] product atom-mapping number 2 found multiple times. +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: [16:03:00] product atom-mapping number 4 found multiple times. +74: [16:03:00] product atom-mapping number 3 found multiple times. +74: [16:03:00] product atom-mapping number 2 found multiple times. +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: [16:03:00] product atom-mapping number 4 found multiple times. +74: [16:03:00] product atom-mapping number 3 found multiple times. +74: [16:03:00] product atom-mapping number 2 found multiple times. +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: [16:03:00] product atom-mapping number 3 found multiple times. +74: [16:03:00] product atom-mapping number 2 found multiple times. +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: [16:03:00] mapped atoms in the reactants were not mapped in the products. +74: unmapped numbers are: 4 +74: [16:03:00] product atom-mapping number 3 found multiple times. +74: [16:03:00] product atom-mapping number 2 found multiple times. +74: [16:03:00] product atom-mapping number 1 found multiple times. +74: [16:03:00] mapped atoms in the reactants were not mapped in the products. +74: unmapped numbers are: 4 +74: [16:03:00] product atom-mapping number 6 not found in reactants. +74: [16:03:00] product atom-mapping number 7 not found in reactants. +74: [16:03:00] product atom-mapping number 8 not found in reactants. +74: [16:03:00] product atom-mapping number 7 not found in reactants. +74: [16:03:00] product atom-mapping number 8 not found in reactants. +74: [16:03:00] product atom-mapping number 9 not found in reactants. +74: [16:03:00] product atom-mapping number 10 not found in reactants. +74: [16:03:00] mapped atoms in the reactants were not mapped in the products. +74: unmapped numbers are: 6 +74: [16:03:00] product atom-mapping number 7 not found in reactants. +74: [16:03:00] product atom-mapping number 8 not found in reactants. +74: [16:03:00] product atom-mapping number 9 not found in reactants. +74: [16:03:00] product atom-mapping number 10 not found in reactants. +74: [16:03:00] mapped atoms in the reactants were not mapped in the products. +74: unmapped numbers are: 6 +74: 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] +74: 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] +75: [16:03:00] ------------------------------------- +75: [16:03:00] Test Reaction DifferenceFingerprint + 69/208 Test #75: testReactionFingerprints ............... Passed 0.06 sec +test 76 + Start 76: testEnumeration + +76: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration +76: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions +76: Test timeout computed to be: 1500 +74: [16:03:00] mapped atoms in the reactants were not mapped in the products. +74: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 +74: [16:03:01] product atom-mapping number 17 not found in reactants. +74: [16:03:01] product atom-mapping number 18 not found in reactants. +74: [16:03:01] mapped atoms in the reactants were not mapped in the products. +74: unmapped numbers are: 12 +74: [16:03:01] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +74: [16:03:01] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +74: +74: [16:03:01] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels +74: ------------- +74: CCOc1ccccc1 +58: [16:03:01] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [16:03:01] Warning: molecule is tagged as 3D, but all Z coords are zero +76: 30000000 30000000 +58: ---------------------------------- +58: ---------------------------------- +58: [16:03:01] +58: +58: **** +58: Pre-condition Violation +58: rlabel out of range for MDL files +58: Violation occurred on line 804 in file ./Code/GraphMol/Atom.cpp +58: Failed Expression: rlabel >= 0 && rlabel < 100 +58: **** +58: +58: [16:03:01] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +25: Checking against /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +74: [16:03:01] reactant 0 has no mapped atoms. +74: [16:03:01] product 0 has no mapped atoms. +74: [16:03:01] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. + 70/208 Test #74: testReaction ........................... Passed 0.64 sec +test 77 + Start 77: rxnTestCatch + +77: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch +77: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions +77: Test timeout computed to be: 1500 +77: [16:03:01] atom 0 in product 0 has multiple charge specifications. +77: [16:03:01] mapped atoms in the reactants were not mapped in the products. +77: unmapped numbers are: 2 +77: [16:03:01] mapped atoms in the reactants were not mapped in the products. +77: unmapped numbers are: 2 +77: [16:03:01] SMARTS Parse Error: unclosed ring for input: 'CC1' +77: [16:03:01] SMILES Parse Error: unclosed ring for input: 'CC1' +77: [16:03:01] mapped atoms in the reactants were not mapped in the products. +77: unmapped numbers are: 2 +77: [16:03:01] product atom-mapping number 2 not found in reactants. +77: [16:03:01] mapped atoms in the reactants were not mapped in the products. +77: unmapped numbers are: 2 +77: [16:03:01] product atom-mapping number 2 not found in reactants. +77: [16:03:01] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +77: =============================================================================== +77: All tests passed (450 assertions in 14 test cases) +77: + 71/208 Test #77: rxnTestCatch ........................... Passed 0.11 sec +test 78 + Start 78: pyChemReactions + +78: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" +78: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap +78: Test timeout computed to be: 1500 +25: All 191 tests passed +58: [16:03:01] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +58: [16:03:01] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +58: [16:03:01] Empty atom list: 'M ALS 1 0 F' on line 8. +25: +25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... +58: de_DE.UTF-8 +58: [16:03:01] ------------------------------------- +58: [16:03:01] Test multithreading Locale Switching +58: [16:03:01] Test multithreading (Done) +58: [16:03:01] ------------------------------------- +58: *************************************** +58: *************************************** +58: [16:03:01] bond with order 0 found on line 7. This is not part of the MDL specification. +58: [16:03:01] unrecognized query bond type, 9, found on line 7. Using an "any" query. +58: [16:03:01] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +58: [16:03:01] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +58: [16:03:01] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [16:03:01] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [16:03:01] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [16:03:01] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [16:03:01] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [16:03:01] Warning: molecule is tagged as 3D, but all Z coords are zero +58: generating smiles +58: 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 +58: converting back +58: check isomorphism +78: [16:03:01] 78: 78: **** 78: Pre-condition Violation @@ -21246,7 +21418,7 @@ 78: Failed Expression: d_implicitValence > -1 78: **** 78: -78: [19:37:06] +78: [16:03:01] 78: 78: **** 78: Pre-condition Violation @@ -21255,180 +21427,190 @@ 78: Failed Expression: d_implicitValence > -1 78: **** 78: - 67/208 Test #81: testChemTransforms ..................... Passed 0.12 sec -test 83 - Start 83: tautomerQueryTestCatch - -83: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch -83: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery -83: Test timeout computed to be: 1500 -78: ...[19:37:06] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -78: [19:37:06] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -78: [19:37:06] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -78: [19:37:06] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -78: .[19:37:06] product atom-mapping number 1 found multiple times. -78: [19:37:06] product atom-mapping number 1 found multiple times. -82: [19:37:06] Incomplete atom labelling, cannot make bond -82: [19:37:06] -82: -82: **** -82: Invariant Violation -82: molzip: bond info already exists for end atom with label:1 -82: Violation occurred on line 982 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -82: Failed Expression: !bond.b -82: **** -82: -82: [19:37:06] Incomplete atom labelling, cannot make bond -82: [19:37:06] -82: -82: **** -82: Invariant Violation -82: molzip: bond info already exists for end atom with label:1 -82: Violation occurred on line 982 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -82: Failed Expression: !bond.b -82: **** -82: -82: [19:37:06] Incomplete atom labelling, cannot make bond -82: [19:37:06] -82: -82: **** -82: Invariant Violation -82: molzip: bond info already exists for end atom with label:1 -82: Violation occurred on line 982 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -82: Failed Expression: !bond.b -82: **** -82: -78: ................[19:37:06] mapped atoms in the reactants were not mapped in the products. +78: ...[16:03:01] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +78: [16:03:01] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +78: [16:03:01] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +78: [16:03:01] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +78: .[16:03:01] product atom-mapping number 1 found multiple times. +78: [16:03:01] product atom-mapping number 1 found multiple times. +78: ................[16:03:01] mapped atoms in the reactants were not mapped in the products. 78: unmapped numbers are: 3 -78: [19:37:06] mapped atoms in the reactants were not mapped in the products. +78: [16:03:01] mapped atoms in the reactants were not mapped in the products. 78: unmapped numbers are: 3 -79: [19:37:06] == testCartesianProduct -74: [19:37:06] reactant 0 has no mapped atoms. -74: [19:37:06] product 0 has no mapped atoms. -74: [19:37:06] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. -78: .[19:37:06] mapped atoms in the reactants were not mapped in the products. +78: .[16:03:02] mapped atoms in the reactants were not mapped in the products. 78: unmapped numbers are: 3 -82: [19:37:06] Incomplete atom labelling, cannot make bond -82: [19:37:06] Incomplete atom labelling, cannot make bond -82: [19:37:06] Incomplete atom labelling, cannot make bond -82: [19:37:06] -82: -82: **** -82: Invariant Violation -82: molzip: bond info already exists for end atom with label:1 -82: Violation occurred on line 982 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -82: Failed Expression: !bond.b -82: **** -82: -79: /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:62: DeprecationWarning: Please use assertEqual instead. -79: self.assertEquals(cartProd.GetNumPermutations(), 10*5*6) - 68/208 Test #74: testReaction ........................... Passed 0.54 sec -test 84 - Start 84: pyTautomerQuery - -84: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" -84: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap -84: Test timeout computed to be: 1500 78: ../build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:515: DeprecationWarning: Please use assertTrue instead. 78: self.failUnless(rxn) -78: [19:37:06] reactant 2 has no mapped atoms. -78: [19:37:06] reactant 2 has no mapped atoms. -78: [19:37:06] product 1 has no mapped atoms. +78: [16:03:02] reactant 2 has no mapped atoms. +78: [16:03:02] reactant 2 has no mapped atoms. +78: [16:03:02] product 1 has no mapped atoms. 78: ../build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:558: DeprecationWarning: Please use assertEqual instead. 78: self.assertEquals(res, res2) -78: ......[19:37:06] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q -78: [19:37:06] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' -78: [19:37:06] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q -78: [19:37:06] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' -78: .[19:37:06] reactant atom-mapping number 1 found multiple times. -78: [19:37:06] product atom-mapping number 2 not found in reactants. -78: [19:37:06] mapped atoms in the reactants were not mapped in the products. +78: ......[16:03:02] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q +78: [16:03:02] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' +78: [16:03:02] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q +78: [16:03:02] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' +78: .[16:03:02] reactant atom-mapping number 1 found multiple times. +78: [16:03:02] product atom-mapping number 2 not found in reactants. +78: [16:03:02] mapped atoms in the reactants were not mapped in the products. 78: unmapped numbers are: 4 -78: [19:37:06] product atom-mapping number 5 not found in reactants. -82: [19:37:06] Incomplete atom labelling, cannot make bond -82: [19:37:06] -82: -82: **** -82: Invariant Violation -82: molzip: bond info already exists for end atom with label:1 -82: Violation occurred on line 982 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -82: Failed Expression: !bond.b -82: **** -82: -82: [19:37:06] -82: -82: **** -82: Invariant Violation -82: molzip: zipped Bond already exists, perhaps labels are duplicated -82: Violation occurred on line 738 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -82: Failed Expression: params.label == MolzipLabel::FragmentOnBonds || !a->getOwningMol().getBondBetweenAtoms(a->getIdx(), b->getIdx()) -82: **** -82: -82: =============================================================================== -82: All tests passed (531 assertions in 4 test cases) -82: -80: .[19:37:06] reactant 0 has no mapped atoms. -80: [19:37:06] product 0 has no mapped atoms. -80: [19:37:06] reactant 0 has no mapped atoms. -80: [19:37:06] product 0 has no mapped atoms. - 69/208 Test #82: chemTransformsTestCatch ................ Passed 0.13 sec -test 85 - Start 85: testSubgraphs1 +78: [16:03:02] product atom-mapping number 5 not found in reactants. +78: ........./build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:739: DeprecationWarning: Please use assertFalse instead. +78: self.failIf(rxn is None) +78: /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> +78: png = open(fname, 'rb').read() +78: ResourceWarning: Enable tracemalloc to get the object allocation traceback +78: ..[16:03:02] SMARTS Parse Error: syntax error while parsing: boromicacid +78: [16:03:02] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +78: [16:03:02] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +78: [16:03:02] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +78: [16:03:02] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +78: [16:03:02] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +78: [16:03:02] reaction has no reactants +78: [16:03:02] reaction has no products +78: [16:03:02] initialization failed +78: [16:03:02] reaction has no reactants +78: [16:03:02] reaction has no products +78: .[16:03:02] SMARTS Parse Error: syntax error while parsing: boromicacid +78: [16:03:02] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +78: [16:03:02] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +78: [16:03:02] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +78: [16:03:02] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +78: [16:03:02] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +78: [16:03:02] reaction has no reactants +78: [16:03:02] reaction has no products +78: [16:03:02] initialization failed +78: [16:03:02] reaction has no reactants +78: [16:03:02] reaction has no products +78: . +78: ---------------------------------------------------------------------- +78: Ran 45 tests in 0.247s +78: +78: OK +78: ******************************************** +78: /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testData/AmideBond.rxn +78: + 72/208 Test #78: pyChemReactions ........................ Passed 0.70 sec +test 79 + Start 79: pyChemReactionEnumerations -85: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 -85: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs -85: Test timeout computed to be: 1500 +79: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" +79: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap +79: Test timeout computed to be: 1500 +79: [16:03:02] == testCartesianProduct +79: /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:62: DeprecationWarning: Please use assertEqual instead. +79: self.assertEquals(cartProd.GetNumPermutations(), 10*5*6) +79: .[16:03:02] == testEnumerateLibrary +79: /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:268: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> +79: enumerator3.InitFromString(open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) +79: ResourceWarning: Enable tracemalloc to get the object allocation traceback +79: ..[16:03:02] == testRGroupState +79: .[16:03:02] == testRandomEnumerateAllBBsLibrary +79: ** [1, 1] +79: ** [0, 2] +79: ** [1, 0] +79: .[16:03:02] == testRandomEnumerateLibrary +79: .[16:03:02] == testRandomSample +79: .[16:03:02] == testRandomSampleAllBBs +79: .[16:03:02] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +79: [16:03:02] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +79: .[16:03:02] == testRemoveBadMatches +79: .[16:03:02] == testTimings +58: [16:03:02] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [16:03:02] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [16:03:02] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [16:03:02] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [16:03:02] deprecated group abbreviation ignored on line 24 +58: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +58: [16:03:02] +58: +58: **** +58: Post-condition Violation +58: Element 'Mv' not found +58: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +58: Failed Expression: anum > -1 +58: **** +58: +79: . +79: ---------------------------------------------------------------------- +79: Ran 11 tests in 2.587s +79: +79: OK +79: True +79: == CartesianProductStrategy CartesianProductStrategy +79: 197 out of 300 +79: 0 6 out of 10 +79: 1 3 out of 5 +79: 2 4 out of 6 +79: 198 out of 300 +79: 0 10 out of 10 +79: 1 5 out of 5 +79: 2 6 out of 6 +79: Skipped 10000000 in 0.11867094039916992 seconds +79: Skipped 10000000 in 1.162139654159546 seconds +79: Skipped 10000000 in 0.7051553726196289 seconds + 73/208 Test #79: pyChemReactionEnumerations ............. Passed 2.92 sec +test 80 + Start 80: pyChemReactionSanitize + +80: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" +80: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap +80: Test timeout computed to be: 1500 +80: .[16:03:05] reactant 0 has no mapped atoms. +80: [16:03:05] product 0 has no mapped atoms. +80: [16:03:05] reactant 0 has no mapped atoms. +80: [16:03:05] product 0 has no mapped atoms. 80: ./build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testSanitize.py:287: DeprecationWarning: Please use assertEqual instead. 80: self.assertEquals(res, good_res) -80: [19:37:06] reactant 0 has no mapped atoms. -80: [19:37:06] reactant 1 has no mapped atoms. -80: [19:37:06] product 0 has no mapped atoms. -80: [19:37:06] reactant 0 has no mapped atoms. -80: [19:37:06] reactant 1 has no mapped atoms. -80: [19:37:06] product 0 has no mapped atoms. -80: [19:37:06] reactant 0 has no mapped atoms. -80: [19:37:06] reactant 1 has no mapped atoms. -80: [19:37:06] product 0 has no mapped atoms. -80: [19:37:06] reactant 0 has no mapped atoms. -80: [19:37:06] reactant 1 has no mapped atoms. -80: [19:37:06] product 0 has no mapped atoms. -80: [19:37:06] reactant 0 has no mapped atoms. -80: [19:37:06] reactant 1 has no mapped atoms. -80: [19:37:06] product 0 has no mapped atoms. -80: [19:37:06] reactant 0 has no mapped atoms. -80: [19:37:06] reactant 1 has no mapped atoms. -80: [19:37:06] product 0 has no mapped atoms. -80: [19:37:06] reactant 0 has no mapped atoms. -80: [19:37:06] reactant 1 has no mapped atoms. -80: [19:37:06] product 0 has no mapped atoms. -80: [19:37:06] reactant 0 has no mapped atoms. -80: [19:37:06] reactant 1 has no mapped atoms. -80: [19:37:06] product 0 has no mapped atoms. -80: [19:37:06] reactant 0 has no mapped atoms. -80: [19:37:06] reactant 1 has no mapped atoms. -80: [19:37:06] product 0 has no mapped atoms. -80: [19:37:06] reactant 0 has no mapped atoms. -80: [19:37:06] reactant 1 has no mapped atoms. -80: [19:37:06] product 0 has no mapped atoms. -80: [19:37:06] reactant 0 has no mapped atoms. -80: [19:37:06] reactant 1 has no mapped atoms. -80: [19:37:06] product 0 has no mapped atoms. -80: [19:37:06] reactant 0 has no mapped atoms. -80: [19:37:06] reactant 1 has no mapped atoms. -80: [19:37:06] product 0 has no mapped atoms. -80: [19:37:06] reactant 0 has no mapped atoms. -80: [19:37:06] reactant 1 has no mapped atoms. -80: [19:37:06] product 0 has no mapped atoms. -80: [19:37:06] reactant 0 has no mapped atoms. -80: [19:37:06] reactant 1 has no mapped atoms. -80: [19:37:06] product 0 has no mapped atoms. -80: [19:37:06] reactant 0 has no mapped atoms. -80: [19:37:06] reactant 1 has no mapped atoms. -80: [19:37:06] product 0 has no mapped atoms. -80: [19:37:06] Could not find RLabel mapping for atom: 0 in template: 1 -80: [19:37:06] reactant 1 has no mapped atoms. -80: [19:37:06] reactant 1 has no mapped atoms. -80: [19:37:06] reactant 1 has no mapped atoms. +80: [16:03:05] reactant 0 has no mapped atoms. +80: [16:03:05] reactant 1 has no mapped atoms. +80: [16:03:05] product 0 has no mapped atoms. +80: [16:03:05] reactant 0 has no mapped atoms. +80: [16:03:05] reactant 1 has no mapped atoms. +80: [16:03:05] product 0 has no mapped atoms. +80: [16:03:05] reactant 0 has no mapped atoms. +80: [16:03:05] reactant 1 has no mapped atoms. +80: [16:03:05] product 0 has no mapped atoms. +80: [16:03:05] reactant 0 has no mapped atoms. +80: [16:03:05] reactant 1 has no mapped atoms. +80: [16:03:05] product 0 has no mapped atoms. +80: [16:03:05] reactant 0 has no mapped atoms. +80: [16:03:05] reactant 1 has no mapped atoms. +80: [16:03:05] product 0 has no mapped atoms. +80: [16:03:05] reactant 0 has no mapped atoms. +80: [16:03:05] reactant 1 has no mapped atoms. +80: [16:03:05] product 0 has no mapped atoms. +80: [16:03:05] reactant 0 has no mapped atoms. +80: [16:03:05] reactant 1 has no mapped atoms. +80: [16:03:05] product 0 has no mapped atoms. +80: [16:03:05] reactant 0 has no mapped atoms. +80: [16:03:05] reactant 1 has no mapped atoms. +80: [16:03:05] product 0 has no mapped atoms. +80: [16:03:05] reactant 0 has no mapped atoms. +80: [16:03:05] reactant 1 has no mapped atoms. +80: [16:03:05] product 0 has no mapped atoms. +80: [16:03:05] reactant 0 has no mapped atoms. +80: [16:03:05] reactant 1 has no mapped atoms. +80: [16:03:05] product 0 has no mapped atoms. +80: [16:03:05] reactant 0 has no mapped atoms. +80: [16:03:05] reactant 1 has no mapped atoms. +80: [16:03:05] product 0 has no mapped atoms. +80: [16:03:05] reactant 0 has no mapped atoms. +80: [16:03:05] reactant 1 has no mapped atoms. +80: [16:03:05] product 0 has no mapped atoms. +80: [16:03:05] reactant 0 has no mapped atoms. +80: [16:03:05] reactant 1 has no mapped atoms. +80: [16:03:05] product 0 has no mapped atoms. +80: [16:03:05] reactant 0 has no mapped atoms. +80: [16:03:05] reactant 1 has no mapped atoms. +80: [16:03:05] product 0 has no mapped atoms. +80: [16:03:05] reactant 0 has no mapped atoms. +80: [16:03:05] reactant 1 has no mapped atoms. +80: [16:03:05] product 0 has no mapped atoms. +80: [16:03:05] Could not find RLabel mapping for atom: 0 in template: 1 +80: [16:03:05] reactant 1 has no mapped atoms. +80: [16:03:05] reactant 1 has no mapped atoms. +80: [16:03:05] reactant 1 has no mapped atoms. 80: () 80: ******************************************** 80: $RXN @@ -21746,11 +21928,6 @@ 80: M END 80: 80: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -85: ----------------------- -85: Subgraph retrieval -85: Finished -85: ----------------------- -85: testSubgraphs2a 80: .. 80: ---------------------------------------------------------------------- 80: Ran 4 tests in 0.030s @@ -21800,20 +21977,164 @@ 80: M END 80: 80: $RXN Failed + 74/208 Test #80: pyChemReactionSanitize ................. Passed 0.38 sec +test 81 + Start 81: testChemTransforms + +81: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms +81: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms +81: Test timeout computed to be: 1500 +81: 1 smi: CC +81: 1 smi: CC +81: 2 smi: CCO[C@H](N)P +81: 2 smi: CC +81: replaceSub smi1:CCP(CC)[C@@H](N)O +81: replaceSub smi1:CCNCC +81: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O +81: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O +81: [16:03:05] SMARTS Parse Error: syntax error while parsing: bar +81: [16:03:05] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' + 75/208 Test #81: testChemTransforms ..................... Passed 0.12 sec +test 82 + Start 82: chemTransformsTestCatch + +82: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +82: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms +82: Test timeout computed to be: 1500 +82: [16:03:05] Incomplete atom labelling, cannot make bond +82: [16:03:05] +82: +82: **** +82: Invariant Violation +82: molzip: bond info already exists for end atom with label:1 +82: Violation occurred on line 982 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +82: Failed Expression: !bond.b +82: **** +82: +82: [16:03:05] Incomplete atom labelling, cannot make bond +82: [16:03:05] +82: +82: **** +82: Invariant Violation +82: molzip: bond info already exists for end atom with label:1 +82: Violation occurred on line 982 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +82: Failed Expression: !bond.b +82: **** +82: +82: [16:03:05] Incomplete atom labelling, cannot make bond +82: [16:03:05] +82: +82: **** +82: Invariant Violation +82: molzip: bond info already exists for end atom with label:1 +82: Violation occurred on line 982 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +82: Failed Expression: !bond.b +82: **** +82: +58: [16:03:05] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [16:03:05] Warning: molecule is tagged as 3D, but all Z coords are zero +82: [16:03:05] Incomplete atom labelling, cannot make bond +82: [16:03:05] Incomplete atom labelling, cannot make bond +82: [16:03:05] Incomplete atom labelling, cannot make bond +82: [16:03:05] +82: +82: **** +82: Invariant Violation +82: molzip: bond info already exists for end atom with label:1 +82: Violation occurred on line 982 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +82: Failed Expression: !bond.b +82: **** +82: +82: [16:03:05] Incomplete atom labelling, cannot make bond +82: [16:03:05] +82: +82: **** +82: Invariant Violation +82: molzip: bond info already exists for end atom with label:1 +82: Violation occurred on line 982 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +82: Failed Expression: !bond.b +82: **** +82: +82: [16:03:05] +82: +82: **** +82: Invariant Violation +82: molzip: zipped Bond already exists, perhaps labels are duplicated +82: Violation occurred on line 738 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +82: Failed Expression: params.label == MolzipLabel::FragmentOnBonds || !a->getOwningMol().getBondBetweenAtoms(a->getIdx(), b->getIdx()) +82: **** +82: +82: =============================================================================== +82: All tests passed (531 assertions in 4 test cases) +82: + 76/208 Test #82: chemTransformsTestCatch ................ Passed 0.15 sec +test 83 + Start 83: tautomerQueryTestCatch + +83: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch +83: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery +83: Test timeout computed to be: 1500 +58: ---------------------------------- +58: ---------------------------------- +58: [16:03:05] +58: +58: **** +58: Pre-condition Violation +58: rlabel out of range for MDL files +58: Violation occurred on line 804 in file ./Code/GraphMol/Atom.cpp +58: Failed Expression: rlabel >= 0 && rlabel < 100 +58: **** +58: +58: [16:03:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +83: =============================================================================== +83: All tests passed (86 assertions in 12 test cases) +83: + 77/208 Test #83: tautomerQueryTestCatch ................. Passed 0.26 sec +test 84 + Start 84: pyTautomerQuery + +84: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" +84: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap +84: Test timeout computed to be: 1500 +58: [16:03:06] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +58: [16:03:06] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +61: [16:03:06] Finished: testSmiCorrectness() +61: [16:03:06] ----------------------------------------- +61: +61: [16:03:06] +61: ----------------------------------------- +61: [16:03:06] Spurious data before the first property will be ignored +61: [16:03:06] Property will be truncated after the first blank line +61: [16:03:06] Property will be truncated after the first blank line +61: [16:03:06] Property will be truncated after the first blank line +58: [16:03:06] Empty atom list: 'M ALS 1 0 F' on line 8. + 78/208 Test #58: fileParsersTest1 ....................... Passed 9.20 sec +test 85 + Start 85: testSubgraphs1 + +85: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 +85: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs +85: Test timeout computed to be: 1500 +85: ----------------------- +85: Subgraph retrieval +85: Finished +85: ----------------------- +85: testSubgraphs2a 85: Finished 85: ----------------------- 85: testSubgraphs2 - 70/208 Test #80: pyChemReactionSanitize ................. Passed 0.33 sec +84: ..... +84: ---------------------------------------------------------------------- +84: Ran 5 tests in 0.050s +84: +84: OK + 79/208 Test #84: pyTautomerQuery ........................ Passed 0.37 sec test 86 Start 86: testSubgraphs2 86: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 86: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs 86: Test timeout computed to be: 1500 -79: .[19:37:06] == testEnumerateLibrary -79: /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:268: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> -79: enumerator3.InitFromString(open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) -79: ResourceWarning: Enable tracemalloc to get the object allocation traceback 86: ----------------------- 86: Test1: pathToSubmol 86: Finished @@ -21828,50 +22149,14 @@ 86: Finished 86: ----------------------- 86: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) -78: ........./build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:739: DeprecationWarning: Please use assertFalse instead. -78: self.failIf(rxn is None) 86: Finished - 71/208 Test #86: testSubgraphs2 ......................... Passed 0.03 sec + 80/208 Test #86: testSubgraphs2 ......................... Passed 0.03 sec test 87 Start 87: filterCatalogTest 87: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest 87: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog 87: Test timeout computed to be: 1500 -78: /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> -78: png = open(fname, 'rb').read() -78: ResourceWarning: Enable tracemalloc to get the object allocation traceback -78: ..[19:37:06] SMARTS Parse Error: syntax error while parsing: boromicacid -78: [19:37:06] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -78: [19:37:06] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -78: [19:37:06] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -78: [19:37:06] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -78: [19:37:06] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -78: [19:37:06] reaction has no reactants -78: [19:37:06] reaction has no products -78: [19:37:06] initialization failed -78: [19:37:06] reaction has no reactants -78: [19:37:06] reaction has no products -78: .[19:37:06] SMARTS Parse Error: syntax error while parsing: boromicacid -78: [19:37:06] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -78: [19:37:06] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -78: [19:37:06] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -78: [19:37:06] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -78: [19:37:06] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -78: [19:37:06] reaction has no reactants -78: [19:37:06] reaction has no products -78: [19:37:06] initialization failed -78: [19:37:06] reaction has no reactants -78: [19:37:06] reaction has no products -78: . -78: ---------------------------------------------------------------------- -78: Ran 45 tests in 0.212s -78: -78: OK -78: ******************************************** -78: /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testData/AmideBond.rxn -78: -79: ..[19:37:06] == testRGroupState 85: Finished 85: ----------------------- 85: Path retrieval @@ -21884,19 +22169,6 @@ 85: Finished 85: ----------------------- 85: testUniqueSubgraphs2 -3: dynamic boost any:1.2447 s -79: .[19:37:06] == testRandomEnumerateAllBBsLibrary -79: ** [1, 1] -79: ** [0, 2] -79: ** [1, 0] - 72/208 Test #78: pyChemReactions ........................ Passed 0.57 sec -test 88 - Start 88: pyFilterCatalog - -88: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" -88: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap -88: Test timeout computed to be: 1500 -79: .[19:37:06] == testRandomEnumerateLibrary 87: Warning: molecule failed filter 87: Warning: molecule failed filter: reason hzone_phenol_A(479) 87: v = { @@ -21923,10 +22195,9 @@ 87: 8,16}, 87: 9,21}, 87: } -79: .[19:37:06] == testRandomSample -83: =============================================================================== -83: All tests passed (86 assertions in 12 test cases) -83: +61: [16:03:06] Finished: testSDCorrectness() +61: [16:03:06] ----------------------------------------- +61: 87: Warning: molecule failed filter 87: Warning: molecule failed filter: reason cyano_imine_B(17) 87: v = { @@ -21959,13 +22230,13 @@ 87: 11,17}, 87: 12,16}, 87: } - 73/208 Test #83: tautomerQueryTestCatch ................. Passed 0.26 sec -test 89 - Start 89: testFragCatalog + 81/208 Test #61: testMultithreadedMolSupplier ........... Passed 7.47 sec +test 88 + Start 88: pyFilterCatalog -89: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -89: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog -89: Test timeout computed to be: 1500 +88: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" +88: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap +88: Test timeout computed to be: 1500 87: Warning: molecule failed filter 87: Warning: molecule failed filter: reason keto_keto_gamma(5) 87: v = { @@ -21996,78 +22267,20 @@ 87: 10,15}, 87: 11,16}, 87: } -3: static RDAny:0.070158 s -58: [19:37:06] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [19:37:06] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [19:37:06] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [19:37:06] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [19:37:06] deprecated group abbreviation ignored on line 24 -89: 21 -58: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -58: [19:37:06] -58: -58: **** -58: Post-condition Violation -58: Element 'Mv' not found -58: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -58: Failed Expression: anum > -1 -58: **** -58: -79: .[19:37:06] == testRandomSampleAllBBs -84: ..... -84: ---------------------------------------------------------------------- -84: Ran 5 tests in 0.050s -84: -84: OK 87: O=C(Cn1cnc2c1c(=O)n(C)c(=O)n2C)N/N=C/c1c(O)ccc2c1cccc2 hzone_phenol_A(479) http://chemistrycompass.com/chemsearch/58909/ 87: FC(F)(F)Oc1ccc(NN=C(C#N)C#N)cc1 cyano_imine_B(17) CHEMBL457504 87: O=C1C2OC2C(=O)c3cc4CCCCc4cc13 keto_keto_gamma(5) CHEMBL476649 - 74/208 Test #84: pyTautomerQuery ........................ Passed 0.29 sec -test 90 - Start 90: pyFragCatalog - -90: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/rough_test.py" -90: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap -90: Test timeout computed to be: 1500 87: 0 hzone_phenol_A(479) 87: 1 cyano_imine_B(17) 87: 2 keto_keto_gamma(5) - 75/208 Test #87: filterCatalogTest ...................... Passed 0.21 sec -test 91 - Start 91: testDescriptors + 82/208 Test #87: filterCatalogTest ...................... Passed 0.24 sec +test 89 + Start 89: testFragCatalog -91: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testDescriptors -91: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors -91: Test timeout computed to be: 1500 -79: .[19:37:06] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -79: [19:37:06] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -79: .[19:37:06] == testRemoveBadMatches -91: [19:37:06] ------------------------------------- -91: [19:37:06] Test Crippen parameter acquisition. -79: .[19:37:06] == testTimings -91: [19:37:06] done -91: [19:37:06] ------------------------------------- -91: [19:37:06] Test Crippen calculation. -91: [19:37:06] done -91: [19:37:06] ------------------------------------- -91: [19:37:06] Test Issue262: problems with Crippen calculation from pickles. -91: [19:37:06] done -91: [19:37:06] ------------------------------------- -91: [19:37:06] Test AMW calculation. -91: [19:37:06] done -91: [19:37:06] ------------------------------------- -91: [19:37:06] Test Exact MW calculation. -91: [19:37:06] done -91: [19:37:06] ------------------------------------- -91: [19:37:06] Test Labute ASA descriptors. -91: [19:37:06] done -91: [19:37:06] ------------------------------------- -91: [19:37:06] Test TPSA descriptors. -88: ../build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/rough_test.py:172: DeprecationWarning: Please use assertEqual instead. -88: self.assertEquals(entry.GetProp(key), "PAINS_A") -91: [19:37:07] done -91: [19:37:07] ------------------------------------- -91: [19:37:07] Test Lipinski parameters. +89: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +89: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog +89: Test timeout computed to be: 1500 +89: 21 85: Finished 85: ----------------------- 85: testRootedSubgraphs @@ -22075,214 +22288,51 @@ 85: ----------------------- 85: testRootedPaths 85: Finished - 76/208 Test #85: testSubgraphs1 ......................... Passed 0.45 sec -test 92 - Start 92: testAUTOCORR2D + 83/208 Test #85: testSubgraphs1 ......................... Passed 0.51 sec +test 90 + Start 90: pyFragCatalog -92: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D -92: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors -92: Test timeout computed to be: 1500 -92: [19:37:07] ---------------------------- -92: start test autocorr2D +90: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/rough_test.py" +90: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap +90: Test timeout computed to be: 1500 +88: ../build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/rough_test.py:172: DeprecationWarning: Please use assertEqual instead. +88: self.assertEquals(entry.GetProp(key), "PAINS_A") 90: ......... 90: ---------------------------------------------------------------------- -90: Ran 9 tests in 0.079s +90: Ran 9 tests in 0.117s 90: 90: OK - 77/208 Test #90: pyFragCatalog .......................... Passed 0.32 sec -test 93 - Start 93: testATF - -93: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testATF -93: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors -93: Test timeout computed to be: 1500 -91: [19:37:07] done -91: [19:37:07] ------------------------------------- -91: [19:37:07] Test VSA descriptors. -91: [19:37:07] done -91: [19:37:07] ------------------------------------- -91: [19:37:07] Test molecular formula calculation. -91: [19:37:07] done -91: [19:37:07] ------------------------------------- -91: [19:37:07] Test Issue 3415534. -91: [19:37:07] done -91: [19:37:07] ------------------------------------- -91: [19:37:07] Test Issue3433771: Bad definition for Crippen atom type O11. -91: [19:37:07] done -91: [19:37:07] ------------------------------------- -91: [19:37:07] Test multithreading -91: reading molecules - 78/208 Test #93: testATF ................................ Passed 0.03 sec -test 94 - Start 94: testBCUT - -94: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testBCUT -94: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors -94: Test timeout computed to be: 1500 -94: [19:37:07] ------------------------------------- -94: [19:37:07] Basic BCUT tests. -91: processing -91: launch :0 -91: launch :1 -91: launch :2 -91: launch :3 -94: [19:37:07] done -94: [19:37:07] ------------------------------------- -94: [19:37:07] Larger BCUT tests. -92: [19:37:07] done -92: [19:37:07] ------------------------------------- -92: [19:37:07] Test Github #3806: NaNs from AUTOCORR2D descriptor -92: [19:37:07] done - 79/208 Test #92: testAUTOCORR2D ......................... Passed 0.42 sec -test 95 - Start 95: testEEM - -95: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testEEM -95: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors -95: Test timeout computed to be: 1500 -3: dynamic RDAny:0.663889 s -3: static RDValue:1e-06 s -3: dynamic RDValue:0.062573 s -3: deleted! -3: [19:37:07] ------------------------------------- -3: [19:37:07] Testing String Pickle Roundtrips. -3: [19:37:07] done -3: [19:37:07] ------------------------------------- -3: [19:37:07] Testing conversion of vect to string. -3: [19:37:07] done -3: [19:37:07] ------------------------------------- -3: [19:37:07] Testing returning const references. -3: [19:37:07] any cast -3: [19:37:07] done: 0.002143 300000 -3: [19:37:07] copy -3: [19:37:07] done: 0.002065 300000 -3: [19:37:07] ref -3: [19:37:07] done: 0.002068 300000 -3: [19:37:07] dict -3: [19:37:07] done: 0.006881 300000 -3: [19:37:07] ref with hasVal -3: [19:37:07] done: 0.002868 300000 -3: [19:37:07] done -3: [19:37:07] ------------------------------------- -3: [19:37:07] Testing dict update. -3: [19:37:07] done -3: deleted! -3: deleted! -3: deleted! -3: deleted! -3: deleted! -3: deleted! - 80/208 Test #3: testDict ............................... Passed 2.54 sec -test 96 - Start 96: testPBF - -96: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testPBF -96: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors -96: Test timeout computed to be: 1500 -96: [19:37:07] ------------------------------------- -96: [19:37:07] Basic PBF tests. -96: [19:37:07] done -96: [19:37:07] ------------------------------------- -96: [19:37:07] PBF edge cases. -96: [19:37:07] done - 81/208 Test #96: testPBF ................................ Passed 0.29 sec -test 97 - Start 97: testRDFcustom + 84/208 Test #90: pyFragCatalog .......................... Passed 0.52 sec +test 91 + Start 91: testDescriptors -97: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom -97: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors -97: Test timeout computed to be: 1500 -88: ...........[19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -88: [19:37:07] SMILES Parse Error: syntax error while parsing: --- -88: [19:37:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [19:37:07] dasfsadf -89: [19:37:07] +91: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testDescriptors +91: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors +91: Test timeout computed to be: 1500 +91: [16:03:07] ------------------------------------- +91: [16:03:07] Test Crippen parameter acquisition. +91: [16:03:07] done +91: [16:03:07] ------------------------------------- +91: [16:03:07] Test Crippen calculation. +91: [16:03:07] done +91: [16:03:07] ------------------------------------- +91: [16:03:07] Test Issue262: problems with Crippen calculation from pickles. +91: [16:03:07] done +91: [16:03:07] ------------------------------------- +91: [16:03:07] Test AMW calculation. +91: [16:03:07] done +91: [16:03:07] ------------------------------------- +91: [16:03:07] Test Exact MW calculation. +91: [16:03:07] done +91: [16:03:07] ------------------------------------- +91: [16:03:07] Test Labute ASA descriptors. +91: [16:03:07] done +91: [16:03:07] ------------------------------------- +91: [16:03:07] Test TPSA descriptors. +91: [16:03:07] done +91: [16:03:07] ------------------------------------- +91: [16:03:07] Test Lipinski parameters. +89: [16:03:07] 89: 89: **** 89: Invariant Violation @@ -22291,7 +22341,7 @@ 89: Failed Expression: token != tokens.end() 89: **** 89: -89: [19:37:07] +89: [16:03:07] 89: 89: **** 89: Invariant Violation @@ -22300,7 +22350,7 @@ 89: Failed Expression: token != tokens.end() 89: **** 89: -89: [19:37:07] +89: [16:03:07] 89: 89: **** 89: Invariant Violation @@ -22309,25 +22359,131 @@ 89: Failed Expression: token != tokens.end() 89: **** 89: - 82/208 Test #89: testFragCatalog ........................ Passed 1.15 sec -test 98 - Start 98: testRDF - -98: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testRDF -98: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors -98: Test timeout computed to be: 1500 - 83/208 Test #94: testBCUT ............................... Passed 0.73 sec -test 99 - Start 99: testMORSE + 85/208 Test #89: testFragCatalog ........................ Passed 0.96 sec +test 92 + Start 92: testAUTOCORR2D -99: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testMORSE -99: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors -99: Test timeout computed to be: 1500 -88: .[19:37:08] SMILES Parse Error: syntax error while parsing: mydoghasfleas -88: [19:37:08] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' +92: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D +92: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors +92: Test timeout computed to be: 1500 +92: [16:03:07] ---------------------------- +92: start test autocorr2D +91: [16:03:07] done +91: [16:03:07] ------------------------------------- +91: [16:03:07] Test VSA descriptors. +91: [16:03:07] done +91: [16:03:07] ------------------------------------- +91: [16:03:07] Test molecular formula calculation. +91: [16:03:07] done +91: [16:03:07] ------------------------------------- +91: [16:03:07] Test Issue 3415534. +91: [16:03:07] done +91: [16:03:07] ------------------------------------- +91: [16:03:07] Test Issue3433771: Bad definition for Crippen atom type O11. +91: [16:03:07] done +91: [16:03:07] ------------------------------------- +91: [16:03:07] Test multithreading +91: reading molecules +91: processing +91: launch :0 +91: launch :1 +91: launch :2 +91: launch :3 +88: ...........[16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: [16:03:07] SMILES Parse Error: syntax error while parsing: --- +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [16:03:07] dasfsadf +88: .[16:03:07] SMILES Parse Error: syntax error while parsing: mydoghasfleas +88: [16:03:07] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' 88: ...... 88: ---------------------------------------------------------------------- -88: Ran 20 tests in 1.053s +88: Ran 20 tests in 1.134s 88: 88: OK 88: (Five aromatic carbons And (Not any of Five aromatic carbons)) @@ -22349,166 +22505,318 @@ 88: 1 88: 2 88: running - 84/208 Test #88: pyFilterCatalog ........................ Passed 1.33 sec -test 100 - Start 100: test3D + 86/208 Test #88: pyFilterCatalog ........................ Passed 1.46 sec +test 93 + Start 93: testATF -100: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/test3D -100: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors -100: Test timeout computed to be: 1500 -100: [19:37:08] ------------------------------------- -100: [19:37:08] Basic PMI tests. +93: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testATF +93: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors +93: Test timeout computed to be: 1500 + 87/208 Test #93: testATF ................................ Passed 0.03 sec +test 94 + Start 94: testBCUT + +94: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testBCUT +94: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors +94: Test timeout computed to be: 1500 +94: [16:03:08] ------------------------------------- +94: [16:03:08] Basic BCUT tests. +94: [16:03:08] done +94: [16:03:08] ------------------------------------- +94: [16:03:08] Larger BCUT tests. +92: [16:03:08] done +92: [16:03:08] ------------------------------------- +92: [16:03:08] Test Github #3806: NaNs from AUTOCORR2D descriptor +92: [16:03:08] done + 88/208 Test #92: testAUTOCORR2D ......................... Passed 0.54 sec +test 95 + Start 95: testEEM + +95: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testEEM +95: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors +95: Test timeout computed to be: 1500 + 89/208 Test #94: testBCUT ............................... Passed 0.81 sec +test 96 + Start 96: testPBF + +96: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testPBF +96: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors +96: Test timeout computed to be: 1500 +96: [16:03:08] ------------------------------------- +96: [16:03:08] Basic PBF tests. 95: =>start test EEM 95: 0 95: 100 95: 200 95: 300 95: 400 -95: Elapsed time: 0.761508 s +95: Elapsed time: 0.902273 s 95: Errors:0 -95: [19:37:08] test on : 500 molecules done - 85/208 Test #95: testEEM ................................ Passed 0.78 sec +95: [16:03:09] test on : 500 molecules done + 90/208 Test #95: testEEM ................................ Passed 0.92 sec +test 97 + Start 97: testRDFcustom + +97: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom +97: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors +97: Test timeout computed to be: 1500 +96: [16:03:09] done +96: [16:03:09] ------------------------------------- +96: [16:03:09] PBF edge cases. +96: [16:03:09] done + 91/208 Test #96: testPBF ................................ Passed 0.34 sec +test 98 + Start 98: testRDF + +98: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testRDF +98: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors +98: Test timeout computed to be: 1500 +25: Checking against /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +25: All 191 tests passed +25: +25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... +97: =>start test rdf custom +97: [16:03:10] test on : 365 molecules done +91: [16:03:10] done +91: [16:03:10] ------------------------------------- +91: [16:03:10] Test Issue252: Bad definitions for Crippen atom types. +91: [16:03:10] done +91: [16:03:10] ------------------------------------- +91: [16:03:10] Test calculation of ChiVs. +91: [16:03:10] done +91: [16:03:10] ------------------------------------- +91: [16:03:10] Test calculation of ChiNs. +91: [16:03:10] done +91: [16:03:10] ------------------------------------- +91: [16:03:10] Test calculation of HallKierAlpha. +91: [16:03:10] done +91: [16:03:10] ------------------------------------- +91: [16:03:10] Test calculation of Kappa1. +91: [16:03:10] done +91: [16:03:10] ------------------------------------- +91: [16:03:10] Test calculation of Kappa2. +91: [16:03:10] done +91: [16:03:10] ------------------------------------- +91: [16:03:10] Test calculation of Kappa3. +91: [16:03:10] done +91: [16:03:10] ------------------------------------- +91: [16:03:10] Test Crippen atom type calculations. +91: [16:03:10] done +91: [16:03:10] ------------------------------------- +91: [16:03:10] Test ring descriptors +91: [16:03:10] done +91: [16:03:10] ------------------------------------- +91: [16:03:10] Test other count descriptors. +91: [16:03:10] done +91: [16:03:10] ------------------------------------- +91: [16:03:10] Test MQN +91: [16:03:10] done +91: [16:03:10] ------------------------------------- +91: [16:03:10] Test GitHub Issue 56. +91: [16:03:10] WARNING: not removing hydrogen atom without neighbors +91: [16:03:10] WARNING: not removing hydrogen atom without neighbors +91: [16:03:10] WARNING: not removing hydrogen atom without neighbors +91: [16:03:10] WARNING: not removing hydrogen atom without neighbors +91: [16:03:10] done +91: [16:03:10] ------------------------------------- +91: [16:03:10] Test Github92: Bad Crippen atom type for pyrrole H. +91: [16:03:10] done +91: [16:03:10] ------------------------------------- +91: [16:03:10] Test Github362: order dependence in Kier-Hall descriptors. +98: =>start test rdf +98: [16:03:10] test on : 365 molecules done +91: [16:03:10] done +91: [16:03:10] ------------------------------------- +91: [16:03:10] Test calculation of spiro and bridgehead counts. +91: [16:03:10] done +91: [16:03:10] ------------------------------------- +91: [16:03:10] Test Github694: ExactMolWt ignoring the mass of the electron +91: [16:03:10] done +91: [16:03:10] ------------------------------------- +91: [16:03:10] Testing Properties and KitchenSink + 92/208 Test #98: testRDF ................................ Passed 1.72 sec +test 99 + Start 99: testMORSE + +99: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testMORSE +99: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors +99: Test timeout computed to be: 1500 +91: [16:03:10] ---Caught keyerror (bad property name)--- +91: [16:03:10] ---Caught stereo value error--- +91: [16:03:10] ------------------------------------- +91: [16:03:10] Test USR Descriptor +91: [16:03:10] done +91: [16:03:10] ------------------------------------- +91: [16:03:10] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required +91: [16:03:10] done +91: [16:03:10] ------------------------------------- +91: [16:03:10] Test Github #1973: support P and S terms for TPSA calculation +91: [16:03:10] done +91: [16:03:10] ------------------------------------- +91: [16:03:10] Test Github #2948: Empty molecule has non-zero LabuteASA +91: [16:03:10] done + 93/208 Test #91: testDescriptors ........................ Passed 3.60 sec +test 100 + Start 100: test3D + +100: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/test3D +100: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors +100: Test timeout computed to be: 1500 +100: [16:03:10] ------------------------------------- +100: [16:03:10] Basic PMI tests. +100: [16:03:11] done +100: [16:03:11] ------------------------------------- +100: [16:03:11] More PMI/NPR tests. +100: [16:03:11] done +100: [16:03:11] ------------------------------------- +100: [16:03:11] Basic NPR tests. +100: [16:03:11] done +100: [16:03:11] ------------------------------------- +100: [16:03:11] PMI edge cases. +100: [16:03:11] done +100: [16:03:11] ------------------------------------- +100: [16:03:11] NPR edge cases. +100: [16:03:11] done +100: [16:03:11] ------------------------------------- +100: [16:03:11] 3D descriptors. +100: [16:03:11] done +100: [16:03:11] ------------------------------------- +100: [16:03:11] 3D descriptor edge cases. +100: [16:03:11] done +100: [16:03:11] ------------------------------------- +100: [16:03:11] Inertial shape factor. +100: [16:03:11] done + 94/208 Test #100: test3D ................................. Passed 0.68 sec test 101 Start 101: testWHIM 101: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testWHIM 101: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 101: Test timeout computed to be: 1500 -25: Checking against /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -100: [19:37:08] done -100: [19:37:08] ------------------------------------- -100: [19:37:08] More PMI/NPR tests. -100: [19:37:08] done -100: [19:37:08] ------------------------------------- -100: [19:37:08] Basic NPR tests. -58: [19:37:08] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [19:37:08] Warning: molecule is tagged as 3D, but all Z coords are zero -25: All 191 tests passed -58: ---------------------------------- -58: ---------------------------------- -58: [19:37:08] -58: -58: **** -58: Pre-condition Violation -58: rlabel out of range for MDL files -58: Violation occurred on line 804 in file ./Code/GraphMol/Atom.cpp -58: Failed Expression: rlabel >= 0 && rlabel < 100 -58: **** -58: -58: [19:37:08] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -25: -25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... -100: [19:37:08] done -100: [19:37:08] ------------------------------------- -100: [19:37:08] PMI edge cases. -100: [19:37:08] done -100: [19:37:08] ------------------------------------- -100: [19:37:08] NPR edge cases. -100: [19:37:08] done -100: [19:37:08] ------------------------------------- -100: [19:37:08] 3D descriptors. -100: [19:37:08] done -100: [19:37:08] ------------------------------------- -100: [19:37:08] 3D descriptor edge cases. -100: [19:37:08] done -100: [19:37:08] ------------------------------------- -100: [19:37:08] Inertial shape factor. -100: [19:37:08] done - 86/208 Test #100: test3D ................................. Passed 0.64 sec +101: =>start test WHIM +101: [16:03:12] test on : 365 molecules done + 95/208 Test #101: testWHIM ............................... Passed 0.50 sec test 102 Start 102: testGETAWAY 102: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY 102: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 102: Test timeout computed to be: 1500 -101: =>start test WHIM -101: [19:37:08] test on : 365 molecules done - 87/208 Test #101: testWHIM ............................... Passed 0.51 sec +99: =>start test MORSE +99: =>read file +99: [16:03:12] test on : 365 molecules done + 96/208 Test #99: testMORSE .............................. Passed 1.37 sec test 103 Start 103: testAUTOCORR3D 103: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D 103: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 103: Test timeout computed to be: 1500 -58: [19:37:08] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -58: [19:37:08] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -58: [19:37:08] Empty atom list: 'M ALS 1 0 F' on line 8. -99: =>start test MORSE -99: =>read file -99: [19:37:08] test on : 365 molecules done - 88/208 Test #99: testMORSE .............................. Passed 1.02 sec +97: =>start test morse custom +97: [16:03:12] test on : 365 molecules done +103: =>start test autocorr3D +103: [16:03:12] test on : 365 molecules done + 97/208 Test #103: testAUTOCORR3D ......................... Passed 0.59 sec test 104 Start 104: testCoulombMat 104: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testCoulombMat 104: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 104: Test timeout computed to be: 1500 -58: de_DE.UTF-8 -58: [19:37:08] ------------------------------------- -58: [19:37:08] Test multithreading Locale Switching -104: ===================== Testing CoulombMat ======================= -104: CM test 1 mat Done - 89/208 Test #104: testCoulombMat ......................... Passed 0.03 sec +76: 0,0 0 +76: 0,1 0 +76: 1,0 0 +76: 1,1 0 +76: 2,0 0 +76: 2,1 0 + 98/208 Test #76: testEnumeration ........................ Passed 11.95 sec test 105 Start 105: descriptorsTestCatch 105: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch 105: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 105: Test timeout computed to be: 1500 - 90/208 Test #37: hanoiTest .............................. Passed 3.64 sec +104: ===================== Testing CoulombMat ======================= +104: CM test 1 mat Done + 99/208 Test #104: testCoulombMat ......................... Passed 0.04 sec test 106 Start 106: pyMolDescriptors 106: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" 106: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/Wrap 106: Test timeout computed to be: 1500 -58: [19:37:09] Test multithreading (Done) -58: [19:37:09] ------------------------------------- -58: *************************************** -58: *************************************** 105: =============================================================================== 105: All tests passed (130 assertions in 5 test cases) 105: - 91/208 Test #105: descriptorsTestCatch ................... Passed 0.05 sec +100/208 Test #105: descriptorsTestCatch ................... Passed 0.04 sec test 107 Start 107: pyMolDescriptors3D 107: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap/test3D.py" 107: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/Wrap 107: Test timeout computed to be: 1500 -58: [19:37:09] bond with order 0 found on line 7. This is not part of the MDL specification. -58: [19:37:09] unrecognized query bond type, 9, found on line 7. Using an "any" query. -58: [19:37:09] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -58: [19:37:09] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -58: [19:37:09] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [19:37:09] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [19:37:09] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [19:37:09] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [19:37:09] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [19:37:09] Warning: molecule is tagged as 3D, but all Z coords are zero -79: . -79: ---------------------------------------------------------------------- -79: Ran 11 tests in 2.552s -79: -79: OK -79: True -79: == CartesianProductStrategy CartesianProductStrategy -79: 197 out of 300 -79: 0 6 out of 10 -79: 1 3 out of 5 -79: 2 4 out of 6 -79: 198 out of 300 -79: 0 10 out of 10 -79: 1 5 out of 5 -79: 2 6 out of 6 -79: Skipped 10000000 in 0.11263489723205566 seconds -79: Skipped 10000000 in 1.2503652572631836 seconds -79: Skipped 10000000 in 0.6582522392272949 seconds -58: generating smiles -58: 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 -58: converting back -58: check isomorphism - 92/208 Test #79: pyChemReactionEnumerations ............. Passed 2.87 sec +97: =>start test AUTOCORR3D custom +97: [16:03:13] test on : 365 molecules done +106: .....[16:03:13] +106: +106: **** +106: Pre-condition Violation +106: Number of atom props not equal to number of atoms +106: Violation occurred on line 83 in file ./Code/GraphMol/Descriptors/BCUT.cpp +106: Failed Expression: atom_props.size() == num_atoms +106: **** +106: +106: ........................ +106: ---------------------------------------------------------------------- +106: Ran 29 tests in 0.052s +106: +106: OK +106: exactmw 78.046950192 +106: amw 78.11399999999999 +106: lipinskiHBA 0.0 +106: lipinskiHBD 0.0 +106: NumRotatableBonds 0.0 +106: NumHBD 0.0 +106: NumHBA 0.0 +106: NumHeavyAtoms 6.0 +106: NumAtoms 6.0 +106: NumHeteroatoms 0.0 +106: NumAmideBonds 0.0 +106: FractionCSP3 0.0 +106: NumRings 1.0 +106: NumAromaticRings 1.0 +106: NumAliphaticRings 0.0 +106: NumSaturatedRings 0.0 +106: NumHeterocycles 0.0 +106: NumAromaticHeterocycles 0.0 +106: NumSaturatedHeterocycles 0.0 +106: NumAliphaticHeterocycles 0.0 +106: NumSpiroAtoms 0.0 +106: NumBridgeheadAtoms 0.0 +106: NumAtomStereoCenters 0.0 +106: NumUnspecifiedAtomStereoCenters 0.0 +106: labuteASA 37.43140311949697 +106: tpsa 0.0 +106: CrippenClogP 1.6865999999999999 +106: CrippenMR 26.442 +106: chi0v 3.4641016151377544 +106: chi1v 1.9999999999999998 +106: chi2v 0.6666666666666665 +106: chi3v 0.6666666666666665 +106: chi4v 0.3849001794597504 +106: chi0n 3.4641016151377544 +106: chi1n 1.9999999999999998 +106: chi2n 0.6666666666666665 +106: chi3n 0.6666666666666665 +106: chi4n 0.3849001794597504 +106: hallKierAlpha -0.78 +106: kappa1 3.4115708812260537 +106: kappa2 1.605769439673522 +106: kappa3 0.582399260140045 +106: Phi 0.9130327103921441 +106: exactmw 78.046950192 +106: lipinskiHBA 0.0 +101/208 Test #106: pyMolDescriptors ....................... Passed 0.45 sec test 108 Start 108: testFingerprints @@ -22998,281 +23306,264 @@ 108: 108: ------------------- 108: -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test Morgan Fingerprints. -108: [19:37:09] done -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test Morgan Fingerprints using fromAtoms argument. -108: [19:37:09] done -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test Morgan Fingerprints as bit vects. -108: [19:37:09] done -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test Morgan Fingerprints with feature invariants. -108: [19:37:09] done -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test additional Morgan fingerprints options. -108: [19:37:09] done -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test Atom Codes. -108: [19:37:09] done -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test Atom Pairs. -108: [19:37:09] done -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test Atom Pairs part 2. -108: [19:37:09] done -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test Topological Torsions. -108: [19:37:09] done -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test Bulk Topological Torsions. -108: [19:37:09] done -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test Hashed Atom Pairs. -108: [19:37:09] done -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test Hashed torsions. -108: [19:37:09] done -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test Rooted Atom Pairs. -108: [19:37:09] done -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test ignoring atoms in Atom Pairs. -108: [19:37:09] done -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test Rooted Topological Torsions. -108: [19:37:09] done -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test ignoring atoms in Topological Torsions. -108: [19:37:09] done -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test atom info from morgan fingerprints. -108: [19:37:09] done -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test atom info from morgan fingerprints including Info Redundant Environments. -108: [19:37:09] done -108: [19:37:09] ------------------------------------- -108: [19:37:09] ------------------------------------- -108: [19:37:09] ------------------------------------- -108: [19:37:09] ------------------------------------- -108: [19:37:09] ------------------------------------- -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test Atom Pairs including info about chirality. -108: [19:37:09] done -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test Topological Torsions including info about chirality. -108: [19:37:09] done -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test GitHub Issue 25: fingerprint backwards compatibility. -108: [19:37:09] done -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test GitHub Issue 151: PatternFingerprint problems -103: =>start test autocorr3D -103: [19:37:09] test on : 365 molecules done - 93/208 Test #103: testAUTOCORR3D ......................... Passed 0.63 sec +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test Morgan Fingerprints. +108: [16:03:13] done +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test Morgan Fingerprints using fromAtoms argument. +108: [16:03:13] done +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test Morgan Fingerprints as bit vects. +108: [16:03:13] done +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test Morgan Fingerprints with feature invariants. +108: [16:03:13] done +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test additional Morgan fingerprints options. +108: [16:03:13] done +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test Atom Codes. +108: [16:03:13] done +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test Atom Pairs. +108: [16:03:13] done +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test Atom Pairs part 2. +108: [16:03:13] done +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test Topological Torsions. +108: [16:03:13] done +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test Bulk Topological Torsions. +97: =>start test 2 WHIM custom +97: [16:03:13] test on : 365 molecules done +107: ........ +107: ---------------------------------------------------------------------- +107: Ran 8 tests in 0.310s +107: +107: OK +102/208 Test #107: pyMolDescriptors3D ..................... Passed 0.62 sec test 109 Start 109: testMHFPFingerprint 109: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint 109: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints 109: Test timeout computed to be: 1500 -108: [19:37:09] done -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test 3D atom pairs. -108: [19:37:09] done -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule -108: [19:37:09] done -108: [19:37:09] ------------------------------------- -108: [19:37:09] Test multithreading with the pattern FP +109: [16:03:13] ------------------------------------- +109: [16:03:13] Test MHFP fingerprint encoder initialization +108: [16:03:13] done +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test Hashed Atom Pairs. +108: [16:03:13] done +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test Hashed torsions. +108: [16:03:13] done +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test Rooted Atom Pairs. +108: [16:03:13] done +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test ignoring atoms in Atom Pairs. +108: [16:03:13] done +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test Rooted Topological Torsions. +108: [16:03:13] done +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test ignoring atoms in Topological Torsions. +108: [16:03:13] done +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test atom info from morgan fingerprints. +108: [16:03:13] done +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test atom info from morgan fingerprints including Info Redundant Environments. +108: [16:03:13] done +108: [16:03:13] ------------------------------------- +108: [16:03:13] ------------------------------------- +108: [16:03:13] ------------------------------------- +108: [16:03:13] ------------------------------------- +108: [16:03:13] ------------------------------------- +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test Atom Pairs including info about chirality. +108: [16:03:13] done +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test Topological Torsions including info about chirality. +108: [16:03:13] done +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test GitHub Issue 25: fingerprint backwards compatibility. +108: [16:03:13] done +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test GitHub Issue 151: PatternFingerprint problems +109: [16:03:13] done +109: [16:03:13] ------------------------------------- +109: [16:03:13] Test MHFP shingling creation +108: [16:03:13] done +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test 3D atom pairs. +108: [16:03:13] done +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule +108: [16:03:13] done +108: [16:03:13] ------------------------------------- +108: [16:03:13] Test multithreading with the pattern FP 108: reading molecules -109: [19:37:09] ------------------------------------- -109: [19:37:09] Test MHFP fingerprint encoder initialization -108: pass 1 -108: launch :0 -108: launch :1 -108: launch :2 -108: launch :3 -109: [19:37:09] done -109: [19:37:09] ------------------------------------- -109: [19:37:09] Test MHFP shingling creation -106: .....[19:37:09] -106: -106: **** -106: Pre-condition Violation -106: Number of atom props not equal to number of atoms -106: Violation occurred on line 83 in file ./Code/GraphMol/Descriptors/BCUT.cpp -106: Failed Expression: atom_props.size() == num_atoms -106: **** -106: -109: [19:37:09] done -109: [19:37:09] ------------------------------------- -109: [19:37:09] Test MHFP hashing of string and uint arrays -109: [19:37:09] done -109: [19:37:09] ------------------------------------- -109: [19:37:09] Test SECFP fingerprint functionality -11: .................. -11: ---------------------------------------------------------------------- -11: Ran 18 tests in 4.143s -11: -11: OK -109: [19:37:09] done - 94/208 Test #109: testMHFPFingerprint .................... Passed 0.09 sec +109: [16:03:13] done +109: [16:03:13] ------------------------------------- +109: [16:03:13] Test MHFP hashing of string and uint arrays +109: [16:03:13] done +109: [16:03:13] ------------------------------------- +109: [16:03:13] Test SECFP fingerprint functionality +109: [16:03:13] done +103/208 Test #109: testMHFPFingerprint .................... Passed 0.08 sec test 110 Start 110: testFingerprintGenerators 110: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators 110: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints 110: Test timeout computed to be: 1500 -106: ........................ -106: ---------------------------------------------------------------------- -106: Ran 29 tests in 0.050s -106: -106: OK -106: exactmw 78.046950192 -106: amw 78.11399999999999 -106: lipinskiHBA 0.0 -106: lipinskiHBD 0.0 -106: NumRotatableBonds 0.0 -106: NumHBD 0.0 -106: NumHBA 0.0 -106: NumHeavyAtoms 6.0 -106: NumAtoms 6.0 -106: NumHeteroatoms 0.0 -106: NumAmideBonds 0.0 -106: FractionCSP3 0.0 -106: NumRings 1.0 -106: NumAromaticRings 1.0 -106: NumAliphaticRings 0.0 -106: NumSaturatedRings 0.0 -106: NumHeterocycles 0.0 -106: NumAromaticHeterocycles 0.0 -106: NumSaturatedHeterocycles 0.0 -106: NumAliphaticHeterocycles 0.0 -106: NumSpiroAtoms 0.0 -106: NumBridgeheadAtoms 0.0 -106: NumAtomStereoCenters 0.0 -106: NumUnspecifiedAtomStereoCenters 0.0 -106: labuteASA 37.43140311949697 -106: tpsa 0.0 -106: CrippenClogP 1.6865999999999999 -106: CrippenMR 26.442 -106: chi0v 3.4641016151377544 -106: chi1v 1.9999999999999998 -106: chi2v 0.6666666666666665 -106: chi3v 0.6666666666666665 -106: chi4v 0.3849001794597504 -106: chi0n 3.4641016151377544 -106: chi1n 1.9999999999999998 -106: chi2n 0.6666666666666665 -106: chi3n 0.6666666666666665 -106: chi4n 0.3849001794597504 -106: hallKierAlpha -0.78 -106: kappa1 3.4115708812260537 -106: kappa2 1.605769439673522 -106: kappa3 0.582399260140045 -106: Phi 0.9130327103921441 -106: exactmw 78.046950192 -106: lipinskiHBA 0.0 - 95/208 Test #11: pyBV ................................... Passed 4.45 sec +108: pass 1 +108: launch :0 +108: launch :1 +108: launch :2 +108: launch :3 +110: [16:03:13] ------------------------------------- +110: [16:03:13] Test atom-pair fp generator +110: [16:03:13] done +110: [16:03:13] ------------------------------------- +110: [16:03:13] Test atom-pair fp generator with different arguments +110: [16:03:13] done +110: [16:03:13] ------------------------------------- +110: [16:03:13] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation +110: [16:03:13] done +110: [16:03:13] ------------------------------------- +110: [16:03:13] Test atom-pair additional output +110: [16:03:13] done +110: [16:03:13] ------------------------------------- +110: [16:03:13] Test Folded Atom Pairs. +110: [16:03:13] done +110: [16:03:13] ------------------------------------- +110: [16:03:13] Test Rooted Atom Pairs. +110: [16:03:13] done +110: [16:03:13] ------------------------------------- +110: [16:03:13] Test ignoring atoms in Atom Pairs. +110: [16:03:13] done +110: [16:03:13] ------------------------------------- +110: [16:03:13] Test Atom Pairs including info about chirality. +110: [16:03:13] done +110: [16:03:13] ------------------------------------- +110: [16:03:13] Test Morgan Fingerprints. +110: [16:03:13] done +110: [16:03:13] ------------------------------------- +110: [16:03:13] Test morgan fp generator +110: [16:03:13] done +110: [16:03:13] ------------------------------------- +110: [16:03:13] Test Morgan Fingerprints using fromAtoms argument. +110: [16:03:13] done +110: [16:03:13] ------------------------------------- +110: [16:03:13] Test Morgan Fingerprints as bit vects. +110: [16:03:13] done +110: [16:03:13] ------------------------------------- +110: [16:03:13] Test Morgan Fingerprints with feature invariants. +110: [16:03:13] done +110: [16:03:13] ------------------------------------- +110: [16:03:13] Test additional Morgan fingerprints options. +110: [16:03:13] done +110: [16:03:13] ------------------------------------- +110: [16:03:13] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +110: [16:03:13] done +110: [16:03:13] ------------------------------------- +110: [16:03:13] Single atoms setting radius 1 bits in Morgan fingerprints +110: [16:03:13] done +110: [16:03:13] ------------------------------------- +110: [16:03:13] Test different invariant generator combinations +110: [16:03:13] done +110: [16:03:13] ------------------------------------- +110: [16:03:13] Test invariant overriding +110: [16:03:13] done +110: [16:03:13] ------------------------------------- +110: [16:03:13] Test RDKit fp generator +108: pass 2 +108: launch :0 +108: launch :1 +108: launch :2 +108: launch :3 +97: =>start test 1 WHIM custom +97: [16:03:13] test on : 365 molecules done +110: [16:03:14] done +110: [16:03:14] ------------------------------------- +110: [16:03:14] Test unfolded version of RDKFP +110: [16:03:14] ------------------------------------- +110: [16:03:14] Test topological torsion fp generator +110: [16:03:14] done +110: [16:03:14] ------------------------------------- +110: [16:03:14] Test Topological Torsions. +110: [16:03:14] done +110: [16:03:14] ------------------------------------- +110: [16:03:14] Test Folded torsions. +110: [16:03:14] done +110: [16:03:14] ------------------------------------- +110: [16:03:14] Test Bulk Topological Torsions. +110: [16:03:14] done +110: [16:03:14] ------------------------------------- +110: [16:03:14] Test Rooted Topological Torsions. +110: [16:03:14] done +110: [16:03:14] ------------------------------------- +110: [16:03:14] Test ignoring atoms in Topological Torsions. +110: [16:03:14] done +110: [16:03:14] ------------------------------------- +110: [16:03:14] ------------------------------------- +110: [16:03:14] Test Topological Torsions including info about chirality. +110: [16:03:14] done +110: [16:03:14] ------------------------------------- +110: [16:03:14] Test GitHub Issue 25: fingerprint backwards compatibility. +110: [16:03:14] done +110: [16:03:14] ------------------------------------- +110: [16:03:14] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +110: [16:03:14] done +110: [16:03:14] ------------------------------------- +110: [16:03:14] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +110: [16:03:14] Warning: molecule is tagged as 3D, but all Z coords are zero +110: [16:03:14] done +110: [16:03:14] ------------------------------------- +110: [16:03:14] Test convenience and bulk fp calculation functions +110: [16:03:14] done +104/208 Test #110: testFingerprintGenerators .............. Passed 1.11 sec test 111 Start 111: fpTestCatch 111: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch 111: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints 111: Test timeout computed to be: 1500 -110: [19:37:09] ------------------------------------- -110: [19:37:09] Test atom-pair fp generator - 96/208 Test #106: pyMolDescriptors ....................... Passed 0.52 sec +111: =============================================================================== +111: All tests passed (163 assertions in 13 test cases) +111: +105/208 Test #111: fpTestCatch ............................ Passed 0.04 sec test 112 Start 112: pyTestGenerator 112: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" 112: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap 112: Test timeout computed to be: 1500 -110: [19:37:09] done -110: [19:37:09] ------------------------------------- -110: [19:37:09] Test atom-pair fp generator with different arguments -110: [19:37:09] done -110: [19:37:09] ------------------------------------- -110: [19:37:09] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation -110: [19:37:09] done -110: [19:37:09] ------------------------------------- -110: [19:37:09] Test atom-pair additional output -110: [19:37:09] done -110: [19:37:09] ------------------------------------- -110: [19:37:09] Test Folded Atom Pairs. -110: [19:37:09] done -110: [19:37:09] ------------------------------------- -110: [19:37:09] Test Rooted Atom Pairs. -110: [19:37:09] done -110: [19:37:09] ------------------------------------- -110: [19:37:09] Test ignoring atoms in Atom Pairs. -110: [19:37:09] done -110: [19:37:09] ------------------------------------- -110: [19:37:09] Test Atom Pairs including info about chirality. -110: [19:37:09] done -110: [19:37:09] ------------------------------------- -110: [19:37:09] Test Morgan Fingerprints. -110: [19:37:09] done -110: [19:37:09] ------------------------------------- -110: [19:37:09] Test morgan fp generator -110: [19:37:09] done -110: [19:37:09] ------------------------------------- -110: [19:37:09] Test Morgan Fingerprints using fromAtoms argument. -110: [19:37:09] done -110: [19:37:09] ------------------------------------- -110: [19:37:09] Test Morgan Fingerprints as bit vects. -110: [19:37:09] done -110: [19:37:09] ------------------------------------- -110: [19:37:09] Test Morgan Fingerprints with feature invariants. -110: [19:37:09] done -110: [19:37:09] ------------------------------------- -110: [19:37:09] Test additional Morgan fingerprints options. -110: [19:37:09] done -110: [19:37:09] ------------------------------------- -110: [19:37:09] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -110: [19:37:09] done -110: [19:37:09] ------------------------------------- -110: [19:37:09] Single atoms setting radius 1 bits in Morgan fingerprints -110: [19:37:09] done -110: [19:37:09] ------------------------------------- -110: [19:37:09] Test different invariant generator combinations -110: [19:37:09] done -110: [19:37:09] ------------------------------------- -110: [19:37:09] Test invariant overriding -110: [19:37:09] done -110: [19:37:09] ------------------------------------- -110: [19:37:09] Test RDKit fp generator -111: =============================================================================== -111: All tests passed (163 assertions in 13 test cases) -111: - 97/208 Test #111: fpTestCatch ............................ Passed 0.09 sec +112: ......... +112: ---------------------------------------------------------------------- +112: Ran 9 tests in 0.071s +112: +112: OK +106/208 Test #112: pyTestGenerator ........................ Passed 0.36 sec test 113 Start 113: pyTestMHFP 113: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" 113: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap 113: Test timeout computed to be: 1500 -108: pass 2 -108: launch :0 -108: launch :1 -108: launch :2 -108: launch :3 -107: ........ -107: ---------------------------------------------------------------------- -107: Ran 8 tests in 0.275s -107: -107: OK - 98/208 Test #107: pyMolDescriptors3D ..................... Passed 0.70 sec +102: =>start test GETAWAY +102: [16:03:15] test on : 365 molecules done +107/208 Test #102: testGETAWAY ............................ Passed 3.19 sec test 114 Start 114: testPartialCharges 114: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges 114: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges 114: Test timeout computed to be: 1500 - 99/208 Test #114: testPartialCharges ..................... Passed 0.05 sec +108/208 Test #114: testPartialCharges ..................... Passed 0.03 sec test 115 Start 115: pyPartialCharges @@ -23281,42 +23572,16 @@ 115: Test timeout computed to be: 1500 113: . 113: ---------------------------------------------------------------------- -113: Ran 1 test in 0.041s +113: Ran 1 test in 0.044s 113: 113: OK -112: ......... -112: ---------------------------------------------------------------------- -112: Ran 9 tests in 0.062s -112: -112: OK -100/208 Test #113: pyTestMHFP ............................. Passed 0.29 sec +109/208 Test #113: pyTestMHFP ............................. Passed 0.33 sec test 116 Start 116: testMolTransforms 116: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms 116: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms 116: Test timeout computed to be: 1500 -110: [19:37:09] done -110: [19:37:09] ------------------------------------- -110: [19:37:09] Test unfolded version of RDKFP -110: [19:37:09] ------------------------------------- -110: [19:37:09] Test topological torsion fp generator -101/208 Test #112: pyTestGenerator ........................ Passed 0.39 sec -test 117 - Start 117: pyMolTransforms - -117: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" -117: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/Wrap -117: Test timeout computed to be: 1500 -110: [19:37:09] done -110: [19:37:09] ------------------------------------- -110: [19:37:09] Test Topological Torsions. -110: [19:37:09] done -110: [19:37:09] ------------------------------------- -110: [19:37:09] Test Folded torsions. -110: [19:37:09] done -110: [19:37:09] ------------------------------------- -110: [19:37:09] Test Bulk Topological Torsions. 116: *********************************************************** 116: Testing MolTransforms 116: --------------------------------- @@ -23347,122 +23612,50 @@ 116: testWeightedCentroid 116: 116: *********************************************************** -102/208 Test #116: testMolTransforms ...................... Passed 0.08 sec +110/208 Test #116: testMolTransforms ...................... Passed 0.05 sec +test 117 + Start 117: pyMolTransforms + +117: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" +117: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/Wrap +117: Test timeout computed to be: 1500 +115: ....... +115: ---------------------------------------------------------------------- +115: Ran 7 tests in 0.167s +115: +115: OK +111/208 Test #115: pyPartialCharges ....................... Passed 0.46 sec test 118 Start 118: testMMFFForceFieldHelpers 118: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers 118: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 118: Test timeout computed to be: 1500 -91: [19:37:09] done -91: [19:37:09] ------------------------------------- -91: [19:37:09] Test Issue252: Bad definitions for Crippen atom types. -91: [19:37:09] done -91: [19:37:09] ------------------------------------- -91: [19:37:09] Test calculation of ChiVs. -91: [19:37:09] done -91: [19:37:09] ------------------------------------- -91: [19:37:09] Test calculation of ChiNs. -91: [19:37:09] done -91: [19:37:09] ------------------------------------- -91: [19:37:09] Test calculation of HallKierAlpha. -91: [19:37:09] done -91: [19:37:09] ------------------------------------- -91: [19:37:09] Test calculation of Kappa1. -91: [19:37:09] done -91: [19:37:09] ------------------------------------- -91: [19:37:09] Test calculation of Kappa2. -91: [19:37:09] done -91: [19:37:09] ------------------------------------- -91: [19:37:09] Test calculation of Kappa3. -91: [19:37:09] done -91: [19:37:09] ------------------------------------- -91: [19:37:09] Test Crippen atom type calculations. -91: [19:37:09] done -91: [19:37:09] ------------------------------------- -91: [19:37:09] Test ring descriptors -91: [19:37:10] done -91: [19:37:10] ------------------------------------- -91: [19:37:10] Test other count descriptors. -91: [19:37:10] done -91: [19:37:10] ------------------------------------- -91: [19:37:10] Test MQN -118: [19:37:10] ------------------------------------- -118: [19:37:10] Test MMFF atom types. -91: [19:37:10] done -91: [19:37:10] ------------------------------------- -91: [19:37:10] Test GitHub Issue 56. -91: [19:37:10] WARNING: not removing hydrogen atom without neighbors -91: [19:37:10] WARNING: not removing hydrogen atom without neighbors -91: [19:37:10] WARNING: not removing hydrogen atom without neighbors -91: [19:37:10] WARNING: not removing hydrogen atom without neighbors -91: [19:37:10] done -91: [19:37:10] ------------------------------------- -91: [19:37:10] Test Github92: Bad Crippen atom type for pyrrole H. -91: [19:37:10] done -91: [19:37:10] ------------------------------------- -91: [19:37:10] Test Github362: order dependence in Kier-Hall descriptors. -91: [19:37:10] done -91: [19:37:10] ------------------------------------- -91: [19:37:10] Test calculation of spiro and bridgehead counts. -91: [19:37:10] done -91: [19:37:10] ------------------------------------- -91: [19:37:10] Test Github694: ExactMolWt ignoring the mass of the electron -91: [19:37:10] done -91: [19:37:10] ------------------------------------- -91: [19:37:10] Testing Properties and KitchenSink -91: [19:37:10] ---Caught keyerror (bad property name)--- -91: [19:37:10] ---Caught stereo value error--- -91: [19:37:10] ------------------------------------- -91: [19:37:10] Test USR Descriptor -91: [19:37:10] done -91: [19:37:10] ------------------------------------- -91: [19:37:10] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required -91: [19:37:10] done -91: [19:37:10] ------------------------------------- -91: [19:37:10] Test Github #1973: support P and S terms for TPSA calculation -91: [19:37:10] done -91: [19:37:10] ------------------------------------- -91: [19:37:10] Test Github #2948: Empty molecule has non-zero LabuteASA -91: [19:37:10] done -103/208 Test #91: testDescriptors ........................ Passed 3.14 sec +118: [16:03:15] ------------------------------------- +118: [16:03:15] Test MMFF atom types. +118: [16:03:15] done +118: [16:03:15] ------------------------------------- +118: [16:03:15] Testing MMFF builder tools. +118: [16:03:15] done +118: [16:03:15] ------------------------------------- +118: [16:03:15] Testing MMFF builder+minimization. +117: ........ +117: ---------------------------------------------------------------------- +117: Ran 8 tests in 0.113s +117: +117: OK +112/208 Test #117: pyMolTransforms ........................ Passed 0.41 sec test 119 Start 119: testMMFFForceFieldHelpersMultiThread 119: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread 119: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 119: Test timeout computed to be: 1500 -118: [19:37:10] done -118: [19:37:10] ------------------------------------- -118: [19:37:10] Testing MMFF builder tools. -119: [19:37:10] ------------------------------------- -119: [19:37:10] Test MMFF multithreading -118: [19:37:10] done -118: [19:37:10] ------------------------------------- -118: [19:37:10] Testing MMFF builder+minimization. -110: [19:37:10] done -110: [19:37:10] ------------------------------------- -110: [19:37:10] Test Rooted Topological Torsions. -110: [19:37:10] done -110: [19:37:10] ------------------------------------- -110: [19:37:10] Test ignoring atoms in Topological Torsions. -110: [19:37:10] done -110: [19:37:10] ------------------------------------- -110: [19:37:10] ------------------------------------- -110: [19:37:10] Test Topological Torsions including info about chirality. -110: [19:37:10] done -110: [19:37:10] ------------------------------------- -110: [19:37:10] Test GitHub Issue 25: fingerprint backwards compatibility. -110: [19:37:10] done -110: [19:37:10] ------------------------------------- -110: [19:37:10] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -110: [19:37:10] done -110: [19:37:10] ------------------------------------- -110: [19:37:10] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -110: [19:37:10] Warning: molecule is tagged as 3D, but all Z coords are zero -110: [19:37:10] done -110: [19:37:10] ------------------------------------- -110: [19:37:10] Test convenience and bulk fp calculation functions +119: [16:03:15] ------------------------------------- +119: [16:03:15] Test MMFF multithreading +118: [16:03:16] done +118: [16:03:16] ------------------------------------- +118: [16:03:16] Testing Issue239. 119: processing 119: launch :0 119: launch :1 @@ -23487,413 +23680,681 @@ 119: launch :20 119: launch :21 119: launch :22 -104/208 Test #39: resMolSupplierTest ..................... Passed 4.77 sec +119: launch :23 +118: [16:03:16] done +118: [16:03:16] ------------------------------------- +118: [16:03:16] Testing calcEnergy with passed coords. +118: [16:03:16] done +118: [16:03:16] ------------------------------------- +118: [16:03:16] Testing calcGrad. +118: [16:03:16] done +118: [16:03:16] ------------------------------------- +118: [16:03:16] Testing Issue242. +118: [16:03:16] done +118: [16:03:16] ------------------------------------- +118: [16:03:16] Testing github 308: crash during MMFF parameterization . +118: [16:03:16] ------------------------------------- +118: [16:03:16] Testing SFIssue1653802. +118: [16:03:16] done +118: [16:03:16] ------------------------------------- +118: [16:03:16] Testing SFIssue2378119. +118: [16:03:16] done +118: [16:03:16] ------------------------------------- +118: [16:03:16] Test MMFF force-field parameter getters. +118: [16:03:16] ------------------------------------- +118: [16:03:16] Test MMFF multithreading +118: generating reference data +119: done +119: [16:03:16] done +113/208 Test #119: testMMFFForceFieldHelpersMultiThread ... Passed 0.69 sec test 120 Start 120: testUFFForceFieldHelpers 120: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers 120: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF 120: Test timeout computed to be: 1500 -119: launch :23 -118: [19:37:10] done -118: [19:37:10] ------------------------------------- -118: [19:37:10] Testing Issue239. -120: [19:37:10] ------------------------------------- -120: [19:37:10] Test UFF atom labels. -120: [19:37:10] done -120: [19:37:10] ------------------------------------- -120: [19:37:10] Test UFF atom typer. -120: [19:37:10] done -120: [19:37:10] ------------------------------------- -120: [19:37:10] Testing UFF builder tools. -120: [19:37:10] done -120: [19:37:10] ------------------------------------- -120: [19:37:10] Testing UFF builder+minimization. -118: [19:37:10] done -118: [19:37:10] ------------------------------------- -118: [19:37:10] Testing calcEnergy with passed coords. -117: ........ -117: ---------------------------------------------------------------------- -117: Ran 8 tests in 0.060s -117: -117: OK -118: [19:37:10] done -118: [19:37:10] ------------------------------------- -118: [19:37:10] Testing calcGrad. -115: ....... -115: ---------------------------------------------------------------------- -115: Ran 7 tests in 0.188s -115: -115: OK -105/208 Test #117: pyMolTransforms ........................ Passed 0.35 sec +120: [16:03:16] ------------------------------------- +120: [16:03:16] Test UFF atom labels. +120: [16:03:16] done +120: [16:03:16] ------------------------------------- +120: [16:03:16] Test UFF atom typer. +120: [16:03:16] done +120: [16:03:16] ------------------------------------- +120: [16:03:16] Testing UFF builder tools. +120: [16:03:16] done +120: [16:03:16] ------------------------------------- +120: [16:03:16] Testing UFF builder+minimization. +120: [16:03:16] done +120: [16:03:16] ------------------------------------- +120: [16:03:16] Testing UFF special cases. +120: [16:03:16] UFFTYPER: Unrecognized charge state for atom: 0 +120: [16:03:16] done +120: [16:03:16] ------------------------------------- +120: [16:03:16] Testing Issue239. +120: [16:03:16] done +120: [16:03:16] ------------------------------------- +120: [16:03:16] Testing calcEnergy with passed coords. +120: [16:03:16] done +120: [16:03:16] ------------------------------------- +120: [16:03:16] Testing calcGrad. +120: [16:03:16] done +120: [16:03:16] ------------------------------------- +120: [16:03:16] Testing SFIssue1653802. +120: [16:03:16] done +120: [16:03:16] ------------------------------------- +120: [16:03:16] Testing SFIssue2378119. +120: [16:03:16] done +120: [16:03:16] ------------------------------------- +120: [16:03:16] Test UFF force-field parameter getters. +120: [16:03:16] ------------------------------------- +120: [16:03:16] Testing handling missing parameters. +120: [16:03:16] UFFTYPER: Unrecognized hybridization for atom: 0 +120: [16:03:16] UFFTYPER: Unrecognized atom type: Cu+1 (0) +120: [16:03:16] UFFTYPER: Unrecognized hybridization for atom: 0 +120: [16:03:16] UFFTYPER: Unrecognized atom type: Cu+1 (0) +120: [16:03:17] done +120: [16:03:17] ------------------------------------- +120: [16:03:17] Testing SFIssue3009337. +120: [16:03:17] done +120: [16:03:17] ------------------------------------- +120: [16:03:17] Test UFF multithreading +120: generating reference data +118: processing +118: launch :0 +118: launch :1 +118: launch :2 +118: launch :3 +118: [16:03:17] Rep: 0 Mol:0 +118: [16:03:17] Rep: 0 Mol:1 +118: [16:03:17] Rep: 0 Mol:3 +118: [16:03:17] Rep: 0 Mol:2 +118: [16:03:17] Rep: 0 Mol:4 +118: [16:03:17] Rep: 0 Mol:5 +118: [16:03:17] Rep: 0 Mol:9 +118: [16:03:17] Rep: 0 Mol:8 +118: [16:03:17] Rep: 0 Mol:13 +97: =>start test GETAWAY custom +97: [16:03:17] test on : 365 molecules done +114/208 Test #97: testRDFcustom .......................... Passed 8.18 sec test 121 Start 121: testCrystalForceField 121: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField 121: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF 121: Test timeout computed to be: 1500 -58: [19:37:10] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [19:37:10] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [19:37:10] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [19:37:10] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [19:37:10] deprecated group abbreviation ignored on line 24 -58: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -58: [19:37:10] -58: -58: **** -58: Post-condition Violation -58: Element 'Mv' not found -58: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -58: Failed Expression: anum > -1 -58: **** -58: -118: [19:37:10] done -118: [19:37:10] ------------------------------------- -118: [19:37:10] Testing Issue242. +118: [16:03:17] Rep: 0 Mol:12 +118: [16:03:17] Rep: 0 Mol:16 +118: [16:03:17] Rep: 0 Mol:17 +118: [16:03:17] Rep: 0 Mol:6 +118: [16:03:17] Rep: 0 Mol:10 +118: [16:03:17] Rep: 0 Mol:20 121: ------------------------------------- 121: Test CrystalFF torsional term. -106/208 Test #115: pyPartialCharges ....................... Passed 0.48 sec +118: [16:03:17] Rep: 0 Mol:24 +118: [16:03:17] Rep: 0 Mol:28 +118: [16:03:17] Rep: 0 Mol:7 +118: [16:03:17] Rep: 0 Mol:11 +118: [16:03:17] Rep: 0 Mol:15 +118: [16:03:17] Rep: 0 Mol:19 +118: [16:03:17] Rep: 0 Mol:21 +118: [16:03:17] Rep: 0 Mol:14 +118: [16:03:17] Rep: 0 Mol:23 +118: [16:03:17] Rep: 0 Mol:27 +118: [16:03:17] Rep: 0 Mol:25 +118: [16:03:17] Rep: 0 Mol:31 +118: [16:03:17] Rep: 0 Mol:18 +118: [16:03:17] Rep: 0 Mol:29 +118: [16:03:17] Rep: 0 Mol:22 +118: [16:03:17] Rep: 0 Mol:26 +120: processing +120: launch :0 +120: launch :1 +120: launch :2 +120: launch :3 +120: [16:03:17] Rep: 0 Mol:0 +120: [16:03:17] Rep: 0 Mol:3 +120: [16:03:17] Rep: 0 Mol:1 +120: [16:03:17] Rep: 0 Mol:4 +120: [16:03:17] Rep: 0 Mol:2 +120: [16:03:17] Rep: 0 Mol:5 +118: [16:03:17] Rep: 0 Mol:30 +120: [16:03:17] Rep: 0 Mol:9 +120: [16:03:17] Rep: 0 Mol:8 +115/208 Test #121: testCrystalForceField .................. Passed 0.30 sec test 122 Start 122: pyForceFieldHelpers 122: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" 122: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap 122: Test timeout computed to be: 1500 -118: [19:37:10] done -118: [19:37:10] ------------------------------------- -118: [19:37:10] Testing github 308: crash during MMFF parameterization . -118: [19:37:10] ------------------------------------- -118: [19:37:10] Testing SFIssue1653802. -118: [19:37:10] done -118: [19:37:10] ------------------------------------- -118: [19:37:10] Testing SFIssue2378119. -118: [19:37:10] done -118: [19:37:10] ------------------------------------- -118: [19:37:10] Test MMFF force-field parameter getters. -118: [19:37:10] ------------------------------------- -118: [19:37:10] Test MMFF multithreading -120: [19:37:10] done -120: [19:37:10] ------------------------------------- -120: [19:37:10] Testing UFF special cases. -120: [19:37:10] UFFTYPER: Unrecognized charge state for atom: 0 -120: [19:37:10] done -120: [19:37:10] ------------------------------------- -120: [19:37:10] Testing Issue239. -120: [19:37:10] done -120: [19:37:10] ------------------------------------- -120: [19:37:10] Testing calcEnergy with passed coords. -107/208 Test #121: testCrystalForceField .................. Passed 0.14 sec +120: [16:03:17] Rep: 0 Mol:12 +120: [16:03:17] Rep: 0 Mol:16 +120: [16:03:17] Rep: 0 Mol:13 +120: [16:03:17] Rep: 0 Mol:7 +120: [16:03:17] Rep: 0 Mol:11 +120: [16:03:17] Rep: 0 Mol:20 +120: [16:03:17] Rep: 0 Mol:15 +120: [16:03:17] Rep: 0 Mol:19 +120: [16:03:17] Rep: 0 Mol:24 +120: [16:03:17] Rep: 0 Mol:6 +120: [16:03:17] Rep: 0 Mol:28 +120: [16:03:17] Rep: 0 Mol:23 +120: [16:03:17] Rep: 0 Mol:27 +120: [16:03:17] Rep: 0 Mol:17 +118: [16:03:17] Rep: 20 Mol:0 +118: [16:03:17] Rep: 20 Mol:4 +118: [16:03:17] Rep: 20 Mol:8 +120: [16:03:17] Rep: 0 Mol:10 +120: [16:03:17] Rep: 0 Mol:31 +118: [16:03:17] Rep: 20 Mol:12 +118: [16:03:17] Rep: 20 Mol:16 +118: [16:03:17] Rep: 20 Mol:20 +118: [16:03:17] Rep: 20 Mol:24 +118: [16:03:17] Rep: 20 Mol:28 +120: [16:03:17] Rep: 0 Mol:21 +120: [16:03:17] Rep: 0 Mol:25 +120: [16:03:17] Rep: 0 Mol:14 +120: [16:03:17] Rep: 0 Mol:18 +120: [16:03:17] Rep: 0 Mol:29 +120: [16:03:17] Rep: 0 Mol:22 +120: [16:03:17] Rep: 0 Mol:26 +120: [16:03:17] Rep: 0 Mol:30 +118: [16:03:17] Rep: 20 Mol:3 +118: [16:03:17] Rep: 20 Mol:7 +118: [16:03:17] Rep: 20 Mol:11 +118: [16:03:17] Rep: 20 Mol:15 +118: [16:03:17] Rep: 20 Mol:19 +118: [16:03:17] Rep: 20 Mol:23 +118: [16:03:17] Rep: 20 Mol:27 +118: [16:03:17] Rep: 20 Mol:31 +118: [16:03:18] Rep: 20 Mol:1 +118: [16:03:18] Rep: 20 Mol:5 +118: [16:03:18] Rep: 20 Mol:9 +118: [16:03:18] Rep: 20 Mol:13 +118: [16:03:18] Rep: 20 Mol:17 +118: [16:03:18] Rep: 20 Mol:21 +118: [16:03:18] Rep: 20 Mol:25 +118: [16:03:18] Rep: 20 Mol:29 +118: [16:03:18] Rep: 40 Mol:3 +118: [16:03:18] Rep: 40 Mol:7 +118: [16:03:18] Rep: 40 Mol:11 +118: [16:03:18] Rep: 40 Mol:15 +118: [16:03:18] Rep: 40 Mol:19 +118: [16:03:18] Rep: 40 Mol:23 +118: [16:03:18] Rep: 40 Mol:27 +118: [16:03:18] Rep: 40 Mol:31 +118: [16:03:18] Rep: 40 Mol:0 +118: [16:03:18] Rep: 40 Mol:4 +118: [16:03:18] Rep: 20 Mol:2 +118: [16:03:18] Rep: 40 Mol:8 +118: [16:03:18] Rep: 20 Mol:6 +118: [16:03:18] Rep: 20 Mol:10 +118: [16:03:18] Rep: 20 Mol:14 +118: [16:03:18] Rep: 20 Mol:18 +118: [16:03:18] Rep: 40 Mol:12 +118: [16:03:18] Rep: 40 Mol:16 +118: [16:03:18] Rep: 40 Mol:20 +118: [16:03:18] Rep: 40 Mol:24 +118: [16:03:18] Rep: 40 Mol:28 +118: [16:03:18] Rep: 20 Mol:22 +118: [16:03:18] Rep: 20 Mol:26 +118: [16:03:18] Rep: 20 Mol:30 +122: [16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +122: [16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +122: [16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +122: [16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +122: [16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +122: ..[16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +122: [16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +118: [16:03:18] Rep: 60 Mol:3 +118: [16:03:18] Rep: 60 Mol:7 +118: [16:03:18] Rep: 60 Mol:11 +118: [16:03:18] Rep: 60 Mol:15 +118: [16:03:18] Rep: 60 Mol:19 +118: [16:03:18] Rep: 60 Mol:23 +118: [16:03:18] Rep: 60 Mol:27 +122: .[16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +118: [16:03:18] Rep: 60 Mol:31 +120: [16:03:18] Rep: 100 Mol:0 +120: [16:03:18] Rep: 100 Mol:4 +120: [16:03:18] Rep: 100 Mol:8 +120: [16:03:18] Rep: 100 Mol:12 +120: [16:03:18] Rep: 100 Mol:16 +120: [16:03:18] Rep: 100 Mol:20 +120: [16:03:18] Rep: 100 Mol:24 +120: [16:03:18] Rep: 100 Mol:28 +122: .[16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +118: [16:03:18] Rep: 80 Mol:3 +118: [16:03:18] Rep: 80 Mol:7 +118: [16:03:18] Rep: 80 Mol:11 +118: [16:03:18] Rep: 80 Mol:15 +118: [16:03:18] Rep: 80 Mol:19 +118: [16:03:18] Rep: 80 Mol:23 +118: [16:03:18] Rep: 80 Mol:27 +118: [16:03:18] Rep: 80 Mol:31 +122: .[16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +118: [16:03:18] Rep: 40 Mol:1 +118: [16:03:18] Rep: 40 Mol:5 +118: [16:03:18] Rep: 40 Mol:9 +118: [16:03:18] Rep: 40 Mol:13 +118: [16:03:18] Rep: 40 Mol:17 +118: [16:03:18] Rep: 40 Mol:21 +118: [16:03:18] Rep: 40 Mol:25 +118: [16:03:18] Rep: 40 Mol:29 +122: .[16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[16:03:18] UFFTYPER: Unrecognized hybridization for atom: 0 +122: [16:03:18] UFFTYPER: Unrecognized atom type: Cu+1 (0) +122: .[16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +122: [16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +122: [16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +122: [16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +122: [16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +122: [16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +122: ..[16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +122: [16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +122: [16:03:18] Molecule does not have explicit Hs. Consider calling AddHs() +118: [16:03:18] Rep: 60 Mol:0 +118: [16:03:18] Rep: 60 Mol:4 +118: [16:03:18] Rep: 60 Mol:8 +118: [16:03:18] Rep: 60 Mol:12 +118: [16:03:18] Rep: 60 Mol:16 +118: [16:03:18] Rep: 60 Mol:20 +120: [16:03:18] Rep: 100 Mol:3 +120: [16:03:18] Rep: 100 Mol:7 +120: [16:03:18] Rep: 100 Mol:11 +120: [16:03:18] Rep: 100 Mol:15 +120: [16:03:18] Rep: 100 Mol:19 +120: [16:03:18] Rep: 100 Mol:23 +120: [16:03:18] Rep: 100 Mol:27 +120: [16:03:18] Rep: 100 Mol:31 +118: [16:03:18] Rep: 60 Mol:24 +118: [16:03:18] Rep: 60 Mol:28 +118: [16:03:18] Rep: 40 Mol:2 +118: [16:03:18] Rep: 40 Mol:6 +118: [16:03:18] Rep: 40 Mol:10 +118: [16:03:18] Rep: 40 Mol:14 +118: [16:03:18] Rep: 40 Mol:18 +118: [16:03:18] Rep: 40 Mol:22 +118: [16:03:18] Rep: 40 Mol:26 +118: [16:03:18] Rep: 40 Mol:30 +122: ... +122: ---------------------------------------------------------------------- +122: Ran 18 tests in 0.453s +122: +122: OK +116/208 Test #122: pyForceFieldHelpers .................... Passed 1.02 sec test 123 Start 123: testDistGeomHelpers 123: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers 123: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers 123: Test timeout computed to be: 1500 -118: generating reference data -120: [19:37:10] done -120: [19:37:10] ------------------------------------- -120: [19:37:10] Testing calcGrad. -120: [19:37:10] done -120: [19:37:10] ------------------------------------- -120: [19:37:10] Testing SFIssue1653802. -120: [19:37:10] done -120: [19:37:10] ------------------------------------- -120: [19:37:10] Testing SFIssue2378119. -120: [19:37:10] done -120: [19:37:10] ------------------------------------- -120: [19:37:10] Test UFF force-field parameter getters. -120: [19:37:10] ------------------------------------- -120: [19:37:10] Testing handling missing parameters. -120: [19:37:10] UFFTYPER: Unrecognized hybridization for atom: 0 -120: [19:37:10] UFFTYPER: Unrecognized atom type: Cu+1 (0) -120: [19:37:10] UFFTYPER: Unrecognized hybridization for atom: 0 -120: [19:37:10] UFFTYPER: Unrecognized atom type: Cu+1 (0) -120: [19:37:10] done -120: [19:37:10] ------------------------------------- -120: [19:37:10] Testing SFIssue3009337. -120: [19:37:10] done -120: [19:37:10] ------------------------------------- -120: [19:37:10] Test UFF multithreading 123: go 123: ------------------------------------- 123: -120: generating reference data -110: [19:37:10] done -108/208 Test #110: testFingerprintGenerators .............. Passed 1.07 sec +118: [16:03:18] Rep: 60 Mol:1 +118: [16:03:18] Rep: 60 Mol:5 +118: [16:03:18] Rep: 60 Mol:9 +118: [16:03:18] Rep: 60 Mol:13 +118: [16:03:18] Rep: 60 Mol:17 +118: [16:03:18] Rep: 60 Mol:21 +118: [16:03:18] Rep: 60 Mol:25 +118: [16:03:18] Rep: 60 Mol:29 +118: [16:03:18] Rep: 80 Mol:0 +118: [16:03:18] Rep: 80 Mol:4 +118: [16:03:18] Rep: 80 Mol:8 +118: [16:03:18] Rep: 80 Mol:12 +118: [16:03:18] Rep: 80 Mol:16 +118: [16:03:18] Rep: 80 Mol:20 +118: [16:03:18] Rep: 80 Mol:24 +118: [16:03:18] Rep: 80 Mol:28 +118: [16:03:18] Rep: 60 Mol:2 +118: [16:03:18] Rep: 60 Mol:6 +118: [16:03:18] Rep: 60 Mol:10 +118: [16:03:18] Rep: 60 Mol:14 +118: [16:03:18] Rep: 60 Mol:18 +118: [16:03:18] Rep: 60 Mol:22 +118: [16:03:18] Rep: 60 Mol:26 +118: [16:03:18] Rep: 60 Mol:30 +120: [16:03:18] Rep: 100 Mol:1 +120: [16:03:18] Rep: 100 Mol:5 +120: [16:03:18] Rep: 100 Mol:9 +120: [16:03:18] Rep: 100 Mol:13 +120: [16:03:18] Rep: 100 Mol:17 +120: [16:03:18] Rep: 100 Mol:21 +120: [16:03:18] Rep: 100 Mol:25 +120: [16:03:18] Rep: 100 Mol:29 +118: [16:03:18] Rep: 80 Mol:1 +118: [16:03:18] Rep: 80 Mol:5 +118: [16:03:18] Rep: 80 Mol:9 +118: [16:03:18] Rep: 80 Mol:13 +118: [16:03:18] Rep: 80 Mol:17 +118: [16:03:18] Rep: 80 Mol:21 +118: [16:03:18] Rep: 80 Mol:25 +118: [16:03:18] Rep: 80 Mol:29 +108: [16:03:18] done +108: [16:03:18] ------------------------------------- +108: [16:03:18] Test GitHub Issue 258: Bad pattern fingerprint for query molecule +108: [16:03:18] done +108: [16:03:18] ------------------------------------- +108: [16:03:18] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +108: [16:03:18] done +108: [16:03:18] ------------------------------------- +108: [16:03:18] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +108: [16:03:18] done +108: [16:03:18] ------------------------------------- +108: [16:03:18] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +108: [16:03:18] Warning: molecule is tagged as 3D, but all Z coords are zero +108: [16:03:18] done +108: [16:03:18] ------------------------------------- +108: [16:03:18] Test unfolded version of RDKFP +108: [16:03:18] ------------------------------------- +108: [16:03:18] Test bitinfo of RDKFP +108: [16:03:18] ------------------------------------- +108: [16:03:18] Single atoms setting radius 1 bits in Morgan fingerprints +108: [16:03:18] done +108: [16:03:18] ------------------------------------- +108: [16:03:18] Github #879: Pattern fingerprint should set bits for single-atom fragments. +108: [16:03:18] done +108: [16:03:18] ------------------------------------- +108: [16:03:18] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms +108: [16:03:18] done +108: [16:03:18] ------------------------------------- +108: [16:03:18] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False +108: [16:03:18] done +108: [16:03:18] ------------------------------------- +108: [16:03:18] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called +108: [16:03:18] done +108: [16:03:18] ------------------------------------- +108: [16:03:18] Github #2115: BitInfo not complete for RDKFingerprint +108: [16:03:18] done +108: [16:03:18] ------------------------------------- +108: [16:03:18] Github #3723: Fingerprint crash for mols with Zero order bonds +117/208 Test #108: testFingerprints ....................... Passed 5.59 sec test 124 Start 124: distGeomHelpersCatch 124: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch 124: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers 124: Test timeout computed to be: 1500 -122: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -122: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -122: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -122: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -122: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -122: ..[19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -122: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -119: done -119: [19:37:10] done -124: [19:37:10] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, (0, 100, 0, 0, 0, 0) -124: [19:37:10] [NH2][C:1](=[NH2])[NH:2]!@;-[CH2:3][C:4]: 102 101 100 99, (0, 0, 2.5, 0, 0, 0) -124: [19:37:10] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, (0, 0, 4, 0, 0, 0) -124: [19:37:10] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, (0, 0, 4, 0, 0, 0) -124: [19:37:10] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, (0, 0, 4, 0, 0, 0) -124: [19:37:10] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, (0, 0, 4, 0, 0, 0) -124: [19:37:10] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, (0, 0, 4, 0, 0, 0) -124: [19:37:10] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, (0, 0, 4, 0, 0, 0) -124: [19:37:10] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, (0, 0, 4, 0, 0, 0) -124: [19:37:10] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, (0, 0, 7, 0, 0, 0) -124: [19:37:10] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, (0, 0, 7, 0, 0, 0) -124: [19:37:10] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, (0, 0, 7, 0, 0, 0) -124: [19:37:10] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, (0, 0, 7, 0, 0, 0) -124: [19:37:10] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, (0, 0, 7, 0, 0, 0) -124: [19:37:10] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, (0, 0, 7, 0, 0, 0) -124: [19:37:10] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, (0, 0, 7, 0, 0, 0) -124: [19:37:10] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, (0, 0, 7, 0, 0, 0) -124: [19:37:10] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, (-1, -0.5, -0.2, -0.3, 0, -0.3) -124: [19:37:10] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, (0, 3.6, 0, 0, 0, 0) -124: [19:37:10] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, (0, 100, 0, 0, 0, 0) -124: [19:37:10] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, (0, 8, 0, 0, 0, 0) -124: [19:37:10] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, (0, 8, 0, 0, 0, 0) -124: [19:37:10] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, (0, 8, 0, 0, 0, 0) -124: [19:37:10] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, (0, 8, 0, 0, 0, 0) -124: [19:37:10] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, (0, 8, 0, 0, 0, 0) -124: [19:37:10] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, (0, 8, 0, 0, 0, 0) -124: [19:37:10] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, (0, 8, 0, 0, 0, 0) -124: [19:37:10] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, (0, 8, 0, 0, 0, 0) -124: [19:37:10] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, (0, 8, 0, 0, 0, 0) -124: [19:37:10] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, (0, 8, 0, 0, 0, 0) -124: [19:37:10] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, (0, 8, 0, 0, 0, 0) -122: .[19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -109/208 Test #119: testMMFFForceFieldHelpersMultiThread ... Passed 0.64 sec +118: [16:03:19] Rep: 80 Mol:2 +118: [16:03:19] Rep: 80 Mol:6 +118: [16:03:19] Rep: 80 Mol:10 +118: [16:03:19] Rep: 80 Mol:14 +118: [16:03:19] Rep: 80 Mol:18 +118: [16:03:19] Rep: 80 Mol:22 +118: [16:03:19] Rep: 80 Mol:26 +118: [16:03:19] Rep: 80 Mol:30 +124: [16:03:19] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, (0, 100, 0, 0, 0, 0) +124: [16:03:19] [NH2][C:1](=[NH2])[NH:2]!@;-[CH2:3][C:4]: 102 101 100 99, (0, 0, 2.5, 0, 0, 0) +124: [16:03:19] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, (0, 0, 4, 0, 0, 0) +124: [16:03:19] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, (0, 0, 4, 0, 0, 0) +124: [16:03:19] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, (0, 0, 4, 0, 0, 0) +124: [16:03:19] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, (0, 0, 4, 0, 0, 0) +124: [16:03:19] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, (0, 0, 4, 0, 0, 0) +124: [16:03:19] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, (0, 0, 4, 0, 0, 0) +124: [16:03:19] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, (0, 0, 4, 0, 0, 0) +124: [16:03:19] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, (0, 0, 7, 0, 0, 0) +124: [16:03:19] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, (0, 0, 7, 0, 0, 0) +124: [16:03:19] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, (0, 0, 7, 0, 0, 0) +124: [16:03:19] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, (0, 0, 7, 0, 0, 0) +124: [16:03:19] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, (0, 0, 7, 0, 0, 0) +124: [16:03:19] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, (0, 0, 7, 0, 0, 0) +124: [16:03:19] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, (0, 0, 7, 0, 0, 0) +124: [16:03:19] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, (0, 0, 7, 0, 0, 0) +124: [16:03:19] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, (-1, -0.5, -0.2, -0.3, 0, -0.3) +124: [16:03:19] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, (0, 3.6, 0, 0, 0, 0) +124: [16:03:19] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, (0, 100, 0, 0, 0, 0) +124: [16:03:19] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, (0, 8, 0, 0, 0, 0) +124: [16:03:19] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, (0, 8, 0, 0, 0, 0) +124: [16:03:19] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, (0, 8, 0, 0, 0, 0) +124: [16:03:19] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, (0, 8, 0, 0, 0, 0) +124: [16:03:19] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, (0, 8, 0, 0, 0, 0) +124: [16:03:19] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, (0, 8, 0, 0, 0, 0) +124: [16:03:19] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, (0, 8, 0, 0, 0, 0) +124: [16:03:19] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, (0, 8, 0, 0, 0, 0) +124: [16:03:19] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, (0, 8, 0, 0, 0, 0) +124: [16:03:19] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, (0, 8, 0, 0, 0, 0) +124: [16:03:19] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, (0, 8, 0, 0, 0, 0) +124: [16:03:19] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, (0, 0, 4, 0, 0, 0) +124: [16:03:19] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, (5, 0, 0, 0, 0, 0) +124: [16:03:19] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, (5, 0, 0, 0, 0, 0) +124: [16:03:19] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, (5, 0, 0, 0, 0, 0) +124: [16:03:19] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, (5, 0, 0, 0, 0, 0) +124: [16:03:19] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, (5, 0, 0, 0, 0, 0) +124: [16:03:19] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, (5, 0, 0, 0, 0, 0) +124: [16:03:19] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, (5, 0, 0, 0, 0, 0) +124: [16:03:19] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, (5, 0, 0, 0, 0, 0) +124: [16:03:19] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, (100, 0, 0, 0, 0, 0) +124: [16:03:19] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, (0, 0, 1, 0, 0, 0) +124: [16:03:19] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, (0, 0, 1, 0, 0, 0) +124: [16:03:19] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, (0, 0, 1, 0, 0, 0) +124: [16:03:19] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, (0, 0, 1, 0, 0, 0) +124: [16:03:19] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, (0, 10, 0, 0, 0, 0) +124: [16:03:19] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, (0, 0, 4, 0, 0, 0) +124: [16:03:19] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, (0, 0, 4, 0, 0, 0) +124: [16:03:19] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 50 52 53 54, (0, 0, 2, 0, 0, 0) +124: [16:03:19] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 58 59 60 61, (0, 0, 2, 0, 0, 0) +124: [16:03:19] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, (0, 3, 0, 0, 0, 0) +124: [16:03:19] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, (0, 3, 0, 0, 0, 0) +124: [16:03:19] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, (0, 3, 0, 0, 0, 0) +124: [16:03:19] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, (0, 3, 0, 0, 0, 0) +124: [16:03:19] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, (0, 3, 0, 0, 0, 0) +124: [16:03:19] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, (0, 3, 0, 0, 0, 0) +124: [16:03:19] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, (0, 3, 0, 0, 0, 0) +124: [16:03:19] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 96 97 105 106, (0, 3, 0, 0, 0, 0) +124: ----------- +124: [16:03:19] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, (0, 8, 0, 0, 0, 0) +124: [16:03:19] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, (0, 8, 0, 0, 0, 0) +124: [16:03:19] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, (0, 0, 4, 0, 0, 0) +124: [16:03:19] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, (0, 0, 4, 0, 0, 0) +124: [16:03:19] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, (5, 0, 0, 0, 0, 0) +124: [16:03:19] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, (5, 0, 0, 0, 0, 0) +124: [16:03:19] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, (100, 0, 0, 0, 0, 0) +124: [16:03:19] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, (100, 0, 0, 0, 0, 0) +124: [16:03:19] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, (0, 10, 0, 0, 0, 0) +124: [16:03:19] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, (0, 10, 0, 0, 0, 0) +124: [16:03:19] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, (0, 0, 2, 0, 0, 0) +124: [16:03:19] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, (0, 0, 2, 0, 0, 0) +124: [16:03:19] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 7 8 9 10, (0, 0, 2, 0, 0, 0) +124: [16:03:19] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, (0, 0, 1, 0, 0, 0) +124: [16:03:19] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, (0, 0, 1, 0, 0, 0) +124: ----------- +124: [16:03:19] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, (0, 8, 0, 0, 0, 0) +124: [16:03:19] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, (0, 0, 4, 0, 0, 0) +124: [16:03:19] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, (100, 0, 0, 0, 0, 0) +124: [16:03:19] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 15 14 13 12, (0, 10, 0, 0, 0, 0) +124: ----------- +124: ----------- +124: [16:03:19] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, (0, 8, 0, 0, 0, 0) +124: [16:03:19] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, (0, 8, 0, 0, 0, 0) +124: [16:03:19] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, (0, 8, 0, 0, 0, 0) +124: [16:03:19] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, (0, 8, 0, 0, 0, 0) +124: [16:03:19] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, (0, 8, 0, 0, 0, 0) +124: [16:03:19] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, (0, 8, 0, 0, 0, 0) +124: [16:03:19] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, (5, 0, 0, 0, 0, 0) +124: [16:03:19] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, (5, 0, 0, 0, 0, 0) +124: [16:03:19] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, (5, 0, 0, 0, 0, 0) +124: [16:03:19] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, (5, 0, 0, 0, 0, 0) +124: [16:03:19] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, (5, 0, 0, 0, 0, 0) +124: [16:03:19] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, (5, 0, 0, 0, 0, 0) +124: [16:03:19] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 0 1 2 3, (0, 0, 2, 0, 0, 0) +124: [16:03:19] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 4 3 2 1, (0, 0, 2, 0, 0, 0) +124: [16:03:19] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 9 8 10 11, (0, 0, 2, 0, 0, 0) +124: [16:03:19] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 12 11 10 8, (0, 0, 2, 0, 0, 0) +124: [16:03:19] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 18 17 19 20, (0, 0, 2, 0, 0, 0) +124: [16:03:19] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 21 20 19 17, (0, 0, 2, 0, 0, 0) +118: [16:03:19] done +118: [16:03:19] ------------------------------------- +118: [16:03:19] Test MMFF multithreading2 +120: [16:03:19] Rep: 100 Mol:2 +120: [16:03:19] Rep: 100 Mol:6 +120: [16:03:19] Rep: 100 Mol:10 +120: [16:03:19] Rep: 100 Mol:14 +120: [16:03:19] Rep: 100 Mol:18 +120: [16:03:19] Rep: 100 Mol:22 +120: [16:03:19] Rep: 100 Mol:26 +120: [16:03:19] Rep: 100 Mol:30 +124: [16:03:19] UFFTYPER: Unrecognized atom type: Pt5+2 (1) +124: [16:03:19] UFFTYPER: Unrecognized atom type: N_5 (2) +124: [16:03:19] UFFTYPER: Unrecognized atom type: N_5 (3) +124: [16:03:19] UFFTYPER: Unrecognized atom type: N_5 (2) +124: [16:03:19] UFFTYPER: Unrecognized atom type: N_5 (3) +124: [16:03:19] UFFTYPER: Unrecognized charge state for atom: 1 +124: [16:03:19] UFFTYPER: Unrecognized charge state for atom: 1 +124: [16:03:19] UFFTYPER: Unrecognized charge state for atom: 1 +124: [16:03:19] UFFTYPER: Unrecognized charge state for atom: 5 +124: [16:03:19] UFFTYPER: Unrecognized charge state for atom: 5 +124: [16:03:19] UFFTYPER: Unrecognized charge state for atom: 5 +25: Checking against /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +124: [16:03:20] UFFTYPER: Unrecognized charge state for atom: 6 +124: [16:03:20] UFFTYPER: Unrecognized charge state for atom: 6 +124: [16:03:20] UFFTYPER: Unrecognized charge state for atom: 6 +25: All 191 tests passed +25: done +25: ------------------------------------- +25: Unit tests for all MMFF constraint terms. +25: 10.0003 +25: done +25: ------------------------------------- +25: Unit test for MMFF TorsionConstraint close to 0 degrees. +25: done +25: ------------------------------------- +25: Unit tests for copying MMFF ForceFields. +25: done +25: ------------------------------------- +25: Unit test for MMFF butane scan. +120: [16:03:20] done +120: [16:03:20] ------------------------------------- +120: [16:03:20] Test UFF multithreading2 +118: [16:03:20] done +118: [16:03:20] ------------------------------------- +118: [16:03:20] Test MMFF multithreading3 +25: done +118/208 Test #25: testMMFFForceField ..................... Passed 28.64 sec test 125 Start 125: pyDistGeomHelpers 125: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" 125: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap 125: Test timeout computed to be: 1500 -124: [19:37:10] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, (0, 0, 4, 0, 0, 0) -124: [19:37:10] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, (5, 0, 0, 0, 0, 0) -124: [19:37:10] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, (5, 0, 0, 0, 0, 0) -124: [19:37:10] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, (5, 0, 0, 0, 0, 0) -124: [19:37:10] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, (5, 0, 0, 0, 0, 0) -124: [19:37:10] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, (5, 0, 0, 0, 0, 0) -124: [19:37:10] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, (5, 0, 0, 0, 0, 0) -124: [19:37:10] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, (5, 0, 0, 0, 0, 0) -124: [19:37:10] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, (5, 0, 0, 0, 0, 0) -124: [19:37:10] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, (100, 0, 0, 0, 0, 0) -124: [19:37:10] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, (0, 0, 1, 0, 0, 0) -124: [19:37:10] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, (0, 0, 1, 0, 0, 0) -124: [19:37:10] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, (0, 0, 1, 0, 0, 0) -124: [19:37:10] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, (0, 0, 1, 0, 0, 0) -124: [19:37:10] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, (0, 10, 0, 0, 0, 0) -124: [19:37:10] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, (0, 0, 4, 0, 0, 0) -124: [19:37:10] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, (0, 0, 4, 0, 0, 0) -124: [19:37:10] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 50 52 53 54, (0, 0, 2, 0, 0, 0) -124: [19:37:10] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 58 59 60 61, (0, 0, 2, 0, 0, 0) -124: [19:37:10] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, (0, 3, 0, 0, 0, 0) -124: [19:37:10] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, (0, 3, 0, 0, 0, 0) -124: [19:37:10] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, (0, 3, 0, 0, 0, 0) -124: [19:37:10] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, (0, 3, 0, 0, 0, 0) -124: [19:37:10] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, (0, 3, 0, 0, 0, 0) -124: [19:37:10] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, (0, 3, 0, 0, 0, 0) -124: [19:37:10] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, (0, 3, 0, 0, 0, 0) -124: [19:37:10] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 96 97 105 106, (0, 3, 0, 0, 0, 0) -124: ----------- -124: [19:37:10] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, (0, 8, 0, 0, 0, 0) -124: [19:37:10] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, (0, 8, 0, 0, 0, 0) -124: [19:37:10] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, (0, 0, 4, 0, 0, 0) -124: [19:37:10] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, (0, 0, 4, 0, 0, 0) -124: [19:37:10] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, (5, 0, 0, 0, 0, 0) -124: [19:37:10] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, (5, 0, 0, 0, 0, 0) -124: [19:37:10] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, (100, 0, 0, 0, 0, 0) -124: [19:37:10] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, (100, 0, 0, 0, 0, 0) -122: .[19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -124: [19:37:10] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, (0, 10, 0, 0, 0, 0) -124: [19:37:10] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, (0, 10, 0, 0, 0, 0) -124: [19:37:10] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, (0, 0, 2, 0, 0, 0) -124: [19:37:10] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, (0, 0, 2, 0, 0, 0) -124: [19:37:10] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 7 8 9 10, (0, 0, 2, 0, 0, 0) -124: [19:37:10] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, (0, 0, 1, 0, 0, 0) -124: [19:37:10] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, (0, 0, 1, 0, 0, 0) -124: ----------- -124: [19:37:10] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, (0, 8, 0, 0, 0, 0) -124: [19:37:10] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, (0, 0, 4, 0, 0, 0) -124: [19:37:10] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, (100, 0, 0, 0, 0, 0) -124: [19:37:10] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 15 14 13 12, (0, 10, 0, 0, 0, 0) -124: ----------- -124: ----------- -124: [19:37:10] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, (0, 8, 0, 0, 0, 0) -124: [19:37:10] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, (0, 8, 0, 0, 0, 0) -124: [19:37:10] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, (0, 8, 0, 0, 0, 0) -124: [19:37:10] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, (0, 8, 0, 0, 0, 0) -124: [19:37:10] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, (0, 8, 0, 0, 0, 0) -124: [19:37:10] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, (0, 8, 0, 0, 0, 0) -124: [19:37:10] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, (5, 0, 0, 0, 0, 0) -124: [19:37:10] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, (5, 0, 0, 0, 0, 0) -124: [19:37:10] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, (5, 0, 0, 0, 0, 0) -124: [19:37:10] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, (5, 0, 0, 0, 0, 0) -124: [19:37:10] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, (5, 0, 0, 0, 0, 0) -124: [19:37:10] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, (5, 0, 0, 0, 0, 0) -124: [19:37:10] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 0 1 2 3, (0, 0, 2, 0, 0, 0) -124: [19:37:10] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 4 3 2 1, (0, 0, 2, 0, 0, 0) -124: [19:37:10] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 9 8 10 11, (0, 0, 2, 0, 0, 0) -124: [19:37:10] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 12 11 10 8, (0, 0, 2, 0, 0, 0) -124: [19:37:10] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 18 17 19 20, (0, 0, 2, 0, 0, 0) -124: [19:37:10] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 21 20 19 17, (0, 0, 2, 0, 0, 0) -122: .[19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[19:37:10] UFFTYPER: Unrecognized hybridization for atom: 0 -122: [19:37:10] UFFTYPER: Unrecognized atom type: Cu+1 (0) -122: .[19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -122: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -122: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -122: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -122: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -122: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -122: ..[19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -122: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -122: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -97: =>start test rdf custom -97: [19:37:10] test on : 365 molecules done -122: ... -122: ---------------------------------------------------------------------- -122: Ran 18 tests in 0.222s -122: -122: OK -110/208 Test #122: pyForceFieldHelpers .................... Passed 0.51 sec +125: .[16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: ..[16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: ..[16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: .[16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +120: [16:03:22] done +120: [16:03:22] ------------------------------------- +120: [16:03:22] Test UFF multithreading3 +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +124: [16:03:22] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +124: [16:03:22] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +125: [16:03:22] Molecule does not have explicit Hs. Consider calling AddHs() +124: [16:03:23] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +125: [16:03:23] Molecule does not have explicit Hs. Consider calling AddHs() +118: [16:03:23] done +118: [16:03:23] ------------------------------------- +118: [16:03:23] Testing github 162: Incorrect SMILES after MMFF parameterization . +118: [16:03:23] done +118: [16:03:23] ------------------------------------- +118: [16:03:23] Testing github 224: crash during MMFF parameterization . +118: [16:03:23] done +119/208 Test #118: testMMFFForceFieldHelpers .............. Passed 7.28 sec test 126 Start 126: testMolAlign 126: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/testMolAlign 126: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign 126: Test timeout computed to be: 1500 -124: [19:37:10] UFFTYPER: Unrecognized atom type: Pt5+2 (1) -124: [19:37:10] UFFTYPER: Unrecognized atom type: N_5 (2) -124: [19:37:10] UFFTYPER: Unrecognized atom type: N_5 (3) -124: [19:37:10] UFFTYPER: Unrecognized atom type: N_5 (2) -124: [19:37:10] UFFTYPER: Unrecognized atom type: N_5 (3) -120: processing -120: launch :0 -120: launch :1 -120: launch :2 -120: launch :3 -120: [19:37:10] Rep: 0 Mol:3 -124: [19:37:10] UFFTYPER: Unrecognized charge state for atom: 1 -120: [19:37:10] Rep: 0 Mol:2 -120: [19:37:10] Rep: 0 Mol:1 -120: [19:37:10] Rep: 0 Mol:7 -120: [19:37:10] Rep: 0 Mol:5 -120: [19:37:10] Rep: 0 Mol:11 -120: [19:37:10] Rep: 0 Mol:0 -120: [19:37:10] Rep: 0 Mol:9 -124: [19:37:10] UFFTYPER: Unrecognized charge state for atom: 1 -120: [19:37:10] Rep: 0 Mol:15 -120: [19:37:10] Rep: 0 Mol:19 -120: [19:37:10] Rep: 0 Mol:23 -120: [19:37:10] Rep: 0 Mol:27 -124: [19:37:10] UFFTYPER: Unrecognized charge state for atom: 1 -120: [19:37:10] Rep: 0 Mol:4 -120: [19:37:10] Rep: 0 Mol:31 -120: [19:37:10] Rep: 0 Mol:13 -120: [19:37:10] Rep: 0 Mol:6 -120: [19:37:10] Rep: 0 Mol:10 -120: [19:37:10] Rep: 0 Mol:17 -120: [19:37:10] Rep: 0 Mol:8 -125: .[19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -120: [19:37:10] Rep: 0 Mol:12 -120: [19:37:10] Rep: 0 Mol:16 -125: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -125: ..[19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -120: [19:37:10] Rep: 0 Mol:14 -120: [19:37:10] Rep: 0 Mol:21 -120: [19:37:10] Rep: 0 Mol:18 -120: [19:37:10] Rep: 0 Mol:20 -125: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -120: [19:37:10] Rep: 0 Mol:22 -125: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -120: [19:37:10] Rep: 0 Mol:25 -120: [19:37:10] Rep: 0 Mol:26 -120: [19:37:10] Rep: 0 Mol:24 -125: ..[19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -125: .[19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -120: [19:37:10] Rep: 0 Mol:29 -120: [19:37:10] Rep: 0 Mol:30 -125: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:10] Molecule does not have explicit Hs. Consider calling AddHs() -120: [19:37:10] Rep: 0 Mol:28 -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -124: [19:37:11] UFFTYPER: Unrecognized charge state for atom: 5 -118: processing -118: launch :0 -118: launch :1 -118: launch :2 -118: launch :3 -118: [19:37:11] Rep: 0 Mol:1 -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -118: [19:37:11] Rep: 0 Mol:5 -118: [19:37:11] Rep: 0 Mol:3 -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -124: [19:37:11] UFFTYPER: Unrecognized charge state for atom: 5 -118: [19:37:11] Rep: 0 Mol:9 -118: [19:37:11] Rep: 0 Mol:2 -118: [19:37:11] Rep: 0 Mol:0 -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -118: [19:37:11] Rep: 0 Mol:13 -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -124: [19:37:11] UFFTYPER: Unrecognized charge state for atom: 5 -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:23] Molecule does not have explicit Hs. Consider calling AddHs() +124: [16:03:23] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +125: [16:03:23] Molecule does not have explicit Hs. Consider calling AddHs() +124: [16:03:23] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +124: [16:03:23] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +124: =============================================================================== +124: All tests passed (163 assertions in 5 test cases) +124: +125: [16:03:23] Molecule does not have explicit Hs. Consider calling AddHs() +120/208 Test #124: distGeomHelpersCatch ................... Passed 4.27 sec +test 127 + Start 127: testO3AAlign + +127: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign +127: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign +127: Test timeout computed to be: 1500 +125: [16:03:23] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:23] Molecule does not have explicit Hs. Consider calling AddHs() +125: .[16:03:23] Molecule does not have explicit Hs. Consider calling AddHs() 126: *********************************************************** 126: Testing MolAlign 126: --------------------------------- @@ -23915,192 +24376,115 @@ 126: testIssue241 126: 126: *********************************************************** -111/208 Test #126: testMolAlign ........................... Passed 0.23 sec -test 127 - Start 127: testO3AAlign - -127: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign -127: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign -127: Test timeout computed to be: 1500 -118: [19:37:11] Rep: 0 Mol:17 -118: [19:37:11] Rep: 0 Mol:4 -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -118: [19:37:11] Rep: 0 Mol:21 -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -118: [19:37:11] Rep: 0 Mol:25 -118: [19:37:11] Rep: 0 Mol:6 -118: [19:37:11] Rep: 0 Mol:8 -118: [19:37:11] Rep: 0 Mol:29 -118: [19:37:11] Rep: 0 Mol:10 -118: [19:37:11] Rep: 0 Mol:12 -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -118: [19:37:11] Rep: 0 Mol:16 -118: [19:37:11] Rep: 0 Mol:7 -118: [19:37:11] Rep: 0 Mol:11 -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -118: [19:37:11] Rep: 0 Mol:20 -118: [19:37:11] Rep: 0 Mol:15 -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -118: [19:37:11] Rep: 0 Mol:24 -124: [19:37:11] UFFTYPER: Unrecognized charge state for atom: 6 -118: [19:37:11] Rep: 0 Mol:19 -118: [19:37:11] Rep: 0 Mol:28 -124: [19:37:11] UFFTYPER: Unrecognized charge state for atom: 6 -118: [19:37:11] Rep: 0 Mol:23 -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -118: [19:37:11] Rep: 0 Mol:27 -124: [19:37:11] UFFTYPER: Unrecognized charge state for atom: 6 -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -118: [19:37:11] Rep: 0 Mol:31 -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -118: [19:37:11] Rep: 0 Mol:14 -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -102: =>start test GETAWAY -102: [19:37:11] test on : 365 molecules done -112/208 Test #102: testGETAWAY ............................ Passed 2.56 sec +121/208 Test #126: testMolAlign ........................... Passed 0.44 sec test 128 Start 128: molAlignCatchTest 128: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest 128: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign 128: Test timeout computed to be: 1500 -118: [19:37:11] Rep: 0 Mol:18 -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -118: [19:37:11] Rep: 0 Mol:22 -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() 128: =============================================================================== 128: All tests passed (9 assertions in 1 test case) 128: -118: [19:37:11] Rep: 0 Mol:26 -113/208 Test #128: molAlignCatchTest ...................... Passed 0.08 sec +122/208 Test #128: molAlignCatchTest ...................... Passed 0.06 sec test 129 Start 129: pyMolAlign 129: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" 129: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/Wrap 129: Test timeout computed to be: 1500 -118: [19:37:11] Rep: 20 Mol:1 -118: [19:37:11] Rep: 20 Mol:5 -118: [19:37:11] Rep: 20 Mol:9 -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -118: [19:37:11] Rep: 20 Mol:13 -118: [19:37:11] Rep: 20 Mol:17 -118: [19:37:11] Rep: 20 Mol:21 -118: [19:37:11] Rep: 20 Mol:25 -118: [19:37:11] Rep: 20 Mol:29 -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -118: [19:37:11] Rep: 0 Mol:30 -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -125: .[19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -118: [19:37:11] Rep: 20 Mol:0 -118: [19:37:11] Rep: 20 Mol:4 -118: [19:37:11] Rep: 20 Mol:8 -118: [19:37:11] Rep: 20 Mol:12 -118: [19:37:11] Rep: 20 Mol:16 -118: [19:37:11] Rep: 20 Mol:20 -118: [19:37:11] Rep: 20 Mol:24 -118: [19:37:11] Rep: 20 Mol:28 -118: [19:37:11] Rep: 20 Mol:3 -118: [19:37:11] Rep: 20 Mol:7 -118: [19:37:11] Rep: 20 Mol:11 -118: [19:37:11] Rep: 20 Mol:15 -118: [19:37:11] Rep: 20 Mol:19 -118: [19:37:11] Rep: 20 Mol:23 -118: [19:37:11] Rep: 20 Mol:27 -118: [19:37:11] Rep: 20 Mol:31 -97: =>start test morse custom -97: [19:37:11] test on : 365 molecules done -118: [19:37:11] Rep: 40 Mol:1 -118: [19:37:11] Rep: 40 Mol:5 -118: [19:37:11] Rep: 40 Mol:9 -118: [19:37:11] Rep: 40 Mol:13 -118: [19:37:11] Rep: 40 Mol:17 -118: [19:37:11] Rep: 40 Mol:21 -118: [19:37:11] Rep: 40 Mol:25 -118: [19:37:11] Rep: 40 Mol:29 -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -118: [19:37:11] Rep: 40 Mol:3 -118: [19:37:11] Rep: 40 Mol:7 -118: [19:37:11] Rep: 40 Mol:11 -118: [19:37:11] Rep: 40 Mol:15 -118: [19:37:11] Rep: 40 Mol:19 -118: [19:37:11] Rep: 40 Mol:23 -118: [19:37:11] Rep: 40 Mol:27 -118: [19:37:11] Rep: 40 Mol:31 -98: =>start test rdf -98: [19:37:11] test on : 365 molecules done -114/208 Test #98: testRDF ................................ Passed 3.83 sec +125: [16:03:23] Molecule does not have explicit Hs. Consider calling AddHs() +123: building molecules +123: generating reference data +120: [16:03:24] done +120: [16:03:24] ------------------------------------- +120: [16:03:24] Testing GitHubIssue62. +120: [16:03:24] beta-lactam 39.6387 +120: [16:03:24] cyclopropanone 174.698 +120: [16:03:24] aziridine 337.986 +120: [16:03:24] aziridinone 115.248 +120: [16:03:24] isobutene 2.48217 +120: [16:03:24] acetone 1.91788 +120: [16:03:24] cyclopentanone 10.1648 +120: [16:03:24] cyclopropene 99.4921 +120: [16:03:24] cyclobutene 41.0156 +120: [16:03:24] cyclopropane 267.236 +120: [16:03:24] gamma-lactam 15.7471 +120: [16:03:24] trans-2,3-diphenylcyclopropan-1-one 203.398 +120: [16:03:24] cis-2,3-diphenylcyclopropan-1-one 206.852 +120: [16:03:24] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 +120: [16:03:24] cyclopropylidencyclobutane 218.879 +125: [16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() +120: [16:03:24] diphenylmethylidencyclobutane 79.6139 +120: [16:03:24] done +120: [16:03:24] ------------------------------------- +120: [16:03:24] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. +120: [16:03:24] done +120: [16:03:24] ------------------------------------- +120: [16:03:24] Test square planar complexes +120: [16:03:24] done +120: [16:03:24] ------------------------------------- +120: [16:03:24] Test octahedral complexes +120: [16:03:24] done +123/208 Test #120: testUFFForceFieldHelpers ............... Passed 7.75 sec test 130 Start 130: testFeatures 130: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 130: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures 130: Test timeout computed to be: 1500 -120: [19:37:11] Rep: 100 Mol:3 -120: [19:37:11] Rep: 100 Mol:7 -120: [19:37:11] Rep: 100 Mol:11 -120: [19:37:11] Rep: 100 Mol:15 -120: [19:37:11] Rep: 100 Mol:19 -120: [19:37:11] Rep: 100 Mol:23 -120: [19:37:11] Rep: 100 Mol:27 -120: [19:37:11] Rep: 100 Mol:31 -130: [19:37:11] ------------------------------------- -130: [19:37:11] AtomType parser testing. -130: [19:37:11] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] -130: [19:37:11] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' -130: [19:37:11] done -130: [19:37:11] ------------------------------------- -130: [19:37:11] FeatureDefinition parser testing. -130: [19:37:11] done -130: [19:37:11] ------------------------------------- -130: [19:37:11] Test pulling feat defs from a string. -130: [19:37:11] done -130: [19:37:11] ------------------------------------- -130: [19:37:11] FeatureDef functionality testing. -130: [19:37:11] done -130: [19:37:11] ------------------------------------- -130: [19:37:11] FeatureFactory testing. -130: [19:37:11] 1 -130: [19:37:11] 2 -130: [19:37:11] 3 -130: [19:37:11] 4 -130: [19:37:11] 5 -130: [19:37:11] 6 -130: [19:37:11] done -130: [19:37:11] ------------------------------------- -130: [19:37:11] Feature Location testing. -130: [19:37:11] done -130: [19:37:11] ------------------------------------- -130: [19:37:11] Test building a FeatureFactory from a file -130: [19:37:11] done -130: [19:37:11] ------------------------------------- -130: [19:37:11] Testing Issue 224. -130: [19:37:11] done -130: [19:37:11] ------------------------------------- -130: [19:37:11] Testing Issue 225. -130: [19:37:11] done -130: [19:37:11] ------------------------------------- -130: [19:37:11] Test Issue346 -130: [19:37:11] done -130: [19:37:11] ------------------------------------- -130: [19:37:11] Test Issue347 -130: [19:37:11] done -130: [19:37:11] ------------------------------------- -130: [19:37:11] Testing Issue 348. -130: [19:37:11] SMARTS Parse Error: syntax error while parsing: [C[C] -130: [19:37:11] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' -130: [19:37:11] ------------------------------------- -130: [19:37:11] Testing Nested AtomType definitions. +130: [16:03:24] ------------------------------------- +130: [16:03:24] AtomType parser testing. +130: [16:03:24] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] +130: [16:03:24] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' +130: [16:03:24] done +130: [16:03:24] ------------------------------------- +130: [16:03:24] FeatureDefinition parser testing. +130: [16:03:24] done +130: [16:03:24] ------------------------------------- +130: [16:03:24] Test pulling feat defs from a string. +130: [16:03:24] done +130: [16:03:24] ------------------------------------- +130: [16:03:24] FeatureDef functionality testing. +130: [16:03:24] done +130: [16:03:24] ------------------------------------- +130: [16:03:24] FeatureFactory testing. +130: [16:03:24] 1 +130: [16:03:24] 2 +130: [16:03:24] 3 +130: [16:03:24] 4 +130: [16:03:24] 5 +130: [16:03:24] 6 +130: [16:03:24] done +130: [16:03:24] ------------------------------------- +130: [16:03:24] Feature Location testing. +130: [16:03:24] done +130: [16:03:24] ------------------------------------- +130: [16:03:24] Test building a FeatureFactory from a file +130: [16:03:24] done +130: [16:03:24] ------------------------------------- +130: [16:03:24] Testing Issue 224. +130: [16:03:24] done +130: [16:03:24] ------------------------------------- +130: [16:03:24] Testing Issue 225. +130: [16:03:24] done +130: [16:03:24] ------------------------------------- +130: [16:03:24] Test Issue346 +130: [16:03:24] done +130: [16:03:24] ------------------------------------- +130: [16:03:24] Test Issue347 +130: [16:03:24] done +130: [16:03:24] ------------------------------------- +130: [16:03:24] Testing Issue 348. +130: [16:03:24] SMARTS Parse Error: syntax error while parsing: [C[C] +130: [16:03:24] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' +130: [16:03:24] ------------------------------------- +130: [16:03:24] Testing Nested AtomType definitions. 130: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] -130: [19:37:11] ------------------------------------- -130: [19:37:11] Testing Github Issue #252: crash when calling getPos() with no conformer. -130: [19:37:11] expect a precondition failure message below -130: [19:37:11] +130: [16:03:24] ------------------------------------- +130: [16:03:24] Testing Github Issue #252: crash when calling getPos() with no conformer. +130: [16:03:24] expect a precondition failure message below +130: [16:03:24] 130: 130: **** 130: Pre-condition Violation @@ -24109,133 +24493,42 @@ 130: Failed Expression: dp_mol->getNumConformers() 130: **** 130: -130: [19:37:11] Done -130: [19:37:11] ------------------------------------- -130: [19:37:11] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() -130: [19:37:11] done -115/208 Test #130: testFeatures ........................... Passed 0.06 sec +130: [16:03:24] Done +130: [16:03:24] ------------------------------------- +130: [16:03:24] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() +130: [16:03:24] done +124/208 Test #130: testFeatures ........................... Passed 0.03 sec test 131 Start 131: pyChemicalFeatures 131: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" 131: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap 131: Test timeout computed to be: 1500 -118: [19:37:11] Rep: 40 Mol:0 -118: [19:37:11] Rep: 40 Mol:4 -118: [19:37:11] Rep: 40 Mol:8 -118: [19:37:11] Rep: 40 Mol:12 -118: [19:37:11] Rep: 40 Mol:16 -118: [19:37:11] Rep: 40 Mol:20 -118: [19:37:11] Rep: 40 Mol:24 -118: [19:37:11] Rep: 40 Mol:28 -118: [19:37:11] Rep: 20 Mol:2 -118: [19:37:11] Rep: 20 Mol:6 -118: [19:37:11] Rep: 20 Mol:10 -118: [19:37:11] Rep: 20 Mol:14 -118: [19:37:11] Rep: 20 Mol:18 -118: [19:37:11] Rep: 20 Mol:22 -118: [19:37:11] Rep: 20 Mol:26 -118: [19:37:11] Rep: 20 Mol:30 -61: [19:37:11] Finished: testSmiCorrectness() -61: [19:37:11] ----------------------------------------- -61: -61: [19:37:11] -61: ----------------------------------------- -125: [19:37:11] Molecule does not have explicit Hs. Consider calling AddHs() -118: [19:37:11] Rep: 60 Mol:3 -118: [19:37:11] Rep: 60 Mol:7 -118: [19:37:11] Rep: 60 Mol:11 -118: [19:37:11] Rep: 60 Mol:1 -118: [19:37:11] Rep: 60 Mol:5 -118: [19:37:11] Rep: 60 Mol:9 -118: [19:37:11] Rep: 60 Mol:13 -118: [19:37:11] Rep: 60 Mol:17 -118: [19:37:11] Rep: 60 Mol:15 -118: [19:37:11] Rep: 60 Mol:19 -118: [19:37:11] Rep: 60 Mol:23 -118: [19:37:11] Rep: 60 Mol:27 -118: [19:37:11] Rep: 60 Mol:21 -118: [19:37:11] Rep: 60 Mol:25 -120: [19:37:11] Rep: 100 Mol:1 -120: [19:37:11] Rep: 100 Mol:5 -120: [19:37:11] Rep: 100 Mol:9 -120: [19:37:11] Rep: 100 Mol:13 -120: [19:37:11] Rep: 100 Mol:17 -120: [19:37:11] Rep: 100 Mol:21 -120: [19:37:11] Rep: 100 Mol:25 -120: [19:37:11] Rep: 100 Mol:29 -118: [19:37:11] Rep: 60 Mol:29 -118: [19:37:12] Rep: 60 Mol:31 -61: [19:37:12] Spurious data before the first property will be ignored -61: [19:37:12] Property will be truncated after the first blank line -61: [19:37:12] Property will be truncated after the first blank line -61: [19:37:12] Property will be truncated after the first blank line -58: [19:37:12] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [19:37:12] Warning: molecule is tagged as 3D, but all Z coords are zero +125: [16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() 131: /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py:154: DeprecationWarning: Please use assertTrue instead. 131: self.failUnless(cfac.GetNumFeatureDefs() == 2) 131: /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py:159: DeprecationWarning: Please use assertFalse instead. 131: self.failIf(m) -131: .[19:37:12] Molecule does not have explicit Hs. Consider calling AddHs() +131: .[16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() 131: /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py:48: DeprecationWarning: Please use assertRaises instead. 131: self.failUnlessRaises(IndexError, lambda: cfac.GetMolFeature(mol, 3)) -118: [19:37:12] Rep: 60 Mol:0 -118: [19:37:12] Rep: 60 Mol:4 -118: [19:37:12] Rep: 60 Mol:8 -118: [19:37:12] Rep: 60 Mol:12 -118: [19:37:12] Rep: 60 Mol:16 -118: [19:37:12] Rep: 60 Mol:20 -118: [19:37:12] Rep: 60 Mol:24 -118: [19:37:12] Rep: 60 Mol:28 -131: .[19:37:12] Molecule does not have explicit Hs. Consider calling AddHs() -118: [19:37:12] Rep: 40 Mol:2 -118: [19:37:12] Rep: 40 Mol:6 -118: [19:37:12] Rep: 40 Mol:10 -118: [19:37:12] Rep: 40 Mol:14 -118: [19:37:12] Rep: 40 Mol:18 -118: [19:37:12] Rep: 40 Mol:22 -118: [19:37:12] Rep: 40 Mol:26 -58: ---------------------------------- -58: ---------------------------------- -118: [19:37:12] Rep: 40 Mol:30 -58: [19:37:12] -58: -58: **** -58: Pre-condition Violation -58: rlabel out of range for MDL files -58: Violation occurred on line 804 in file ./Code/GraphMol/Atom.cpp -58: Failed Expression: rlabel >= 0 && rlabel < 100 -58: **** -58: -58: [19:37:12] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -25: Checking against /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -125: [19:37:12] Molecule does not have explicit Hs. Consider calling AddHs() -131: ..[19:37:12] Molecule does not have explicit Hs. Consider calling AddHs() -131: .[19:37:12] Molecule does not have explicit Hs. Consider calling AddHs() -131: .[19:37:12] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] -131: [19:37:12] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' +131: .[16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() +131: ..[16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() +131: .[16:03:24] Molecule does not have explicit Hs. Consider calling AddHs() +131: .[16:03:24] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] +131: [16:03:24] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' 131: ... 131: ---------------------------------------------------------------------- -131: Ran 9 tests in 0.124s +131: Ran 9 tests in 0.131s 131: 131: OK -116/208 Test #131: pyChemicalFeatures ..................... Passed 0.42 sec +125/208 Test #131: pyChemicalFeatures ..................... Passed 0.44 sec test 132 Start 132: testShapeHelpers 132: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/testShapeHelpers 132: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers 132: Test timeout computed to be: 1500 -118: [19:37:12] Rep: 80 Mol:1 -118: [19:37:12] Rep: 80 Mol:5 -118: [19:37:12] Rep: 80 Mol:9 -97: =>start test AUTOCORR3D custom -97: [19:37:12] test on : 365 molecules done -118: [19:37:12] Rep: 80 Mol:13 -118: [19:37:12] Rep: 80 Mol:17 -118: [19:37:12] Rep: 80 Mol:21 -118: [19:37:12] Rep: 80 Mol:25 -118: [19:37:12] Rep: 80 Mol:29 132: *********************************************************** 132: Testing ShapeHelpers 132: --------------------------------- @@ -24248,100 +24541,48 @@ 132: testGithub4364 132: 132: *********************************************************** -118: [19:37:12] Rep: 80 Mol:3 -117/208 Test #132: testShapeHelpers ....................... Passed 0.07 sec +126/208 Test #132: testShapeHelpers ....................... Passed 0.05 sec test 133 Start 133: pyShapeHelpers 133: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" 133: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap 133: Test timeout computed to be: 1500 -120: [19:37:12] Rep: 100 Mol:0 -118: [19:37:12] Rep: 80 Mol:7 -118: [19:37:12] Rep: 80 Mol:11 -118: [19:37:12] Rep: 80 Mol:15 -118: [19:37:12] Rep: 80 Mol:19 -118: [19:37:12] Rep: 80 Mol:23 -118: [19:37:12] Rep: 80 Mol:27 -118: [19:37:12] Rep: 80 Mol:31 -120: [19:37:12] Rep: 100 Mol:4 -120: [19:37:12] Rep: 100 Mol:8 -120: [19:37:12] Rep: 100 Mol:12 -120: [19:37:12] Rep: 100 Mol:16 -120: [19:37:12] Rep: 100 Mol:20 -120: [19:37:12] Rep: 100 Mol:24 -120: [19:37:12] Rep: 100 Mol:28 -25: All 191 tests passed -118: [19:37:12] Rep: 80 Mol:0 -118: [19:37:12] Rep: 80 Mol:4 -118: [19:37:12] Rep: 80 Mol:8 -118: [19:37:12] Rep: 80 Mol:12 -118: [19:37:12] Rep: 80 Mol:16 -118: [19:37:12] Rep: 80 Mol:20 -118: [19:37:12] Rep: 80 Mol:24 -118: [19:37:12] Rep: 80 Mol:28 -120: [19:37:12] Rep: 100 Mol:2 -120: [19:37:12] Rep: 100 Mol:6 -120: [19:37:12] Rep: 100 Mol:10 -120: [19:37:12] Rep: 100 Mol:14 -120: [19:37:12] Rep: 100 Mol:18 -120: [19:37:12] Rep: 100 Mol:22 -120: [19:37:12] Rep: 100 Mol:26 -120: [19:37:12] Rep: 100 Mol:30 -58: [19:37:12] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -58: [19:37:12] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -118: [19:37:12] Rep: 60 Mol:2 -118: [19:37:12] Rep: 60 Mol:6 -118: [19:37:12] Rep: 60 Mol:10 -118: [19:37:12] Rep: 60 Mol:14 -118: [19:37:12] Rep: 60 Mol:18 -118: [19:37:12] Rep: 60 Mol:22 -118: [19:37:12] Rep: 60 Mol:26 -118: [19:37:12] Rep: 60 Mol:30 -125: [19:37:12] Molecule does not have explicit Hs. Consider calling AddHs() -25: -25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... -58: [19:37:12] Empty atom list: 'M ALS 1 0 F' on line 8. -118/208 Test #58: fileParsersTest1 ....................... Passed 6.89 sec +125: [16:03:25] Molecule does not have explicit Hs. Consider calling AddHs() +133: . +133: ---------------------------------------------------------------------- +133: Ran 1 test in 0.121s +133: +133: OK +133: Testing Shape Helpers wrapper +127/208 Test #133: pyShapeHelpers ......................... Passed 0.40 sec test 134 Start 134: testMolCatalog 134: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/testMolCatalog 134: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog 134: Test timeout computed to be: 1500 -97: =>start test 2 WHIM custom -97: [19:37:12] test on : 365 molecules done -119/208 Test #134: testMolCatalog ......................... Passed 0.07 sec +128/208 Test #134: testMolCatalog ......................... Passed 0.03 sec test 135 Start 135: pyMolCatalog 135: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/Wrap/rough_test.py" 135: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/Wrap 135: Test timeout computed to be: 1500 -133: . -133: ---------------------------------------------------------------------- -133: Ran 1 test in 0.098s -133: -133: OK -133: Testing Shape Helpers wrapper -120/208 Test #133: pyShapeHelpers ......................... Passed 0.40 sec +125: [16:03:25] Molecule does not have explicit Hs. Consider calling AddHs() +135: . +135: ---------------------------------------------------------------------- +135: Ran 1 test in 0.015s +135: +135: OK +129/208 Test #135: pyMolCatalog ........................... Passed 0.29 sec test 136 Start 136: moldraw2DTest1 136: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 136: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D 136: Test timeout computed to be: 1500 -118: [19:37:12] Rep: 80 Mol:2 -118: [19:37:12] Rep: 80 Mol:6 -118: [19:37:12] Rep: 80 Mol:10 -118: [19:37:12] Rep: 80 Mol:14 -118: [19:37:12] Rep: 80 Mol:18 -118: [19:37:12] Rep: 80 Mol:22 -118: [19:37:12] Rep: 80 Mol:26 -118: [19:37:12] Rep: 80 Mol:30 136: ----------------- Test 1 -125: [19:37:12] Molecule does not have explicit Hs. Consider calling AddHs() -124: [19:37:12] UFFTYPER: Warning: hybridization set to SP3 for atom 6 136: file test1_5.svg gave hash 3105787089U not the expected 2964125114U 136: file test1_6.svg gave hash 995867455U not the expected 464012122U 136: Done @@ -24353,139 +24594,223 @@ 136: file test4_1.png gave hash 747479389U not the expected 1924202631U 136: Done 136: ----------------- Test 5 -135: . -135: ---------------------------------------------------------------------- -135: Ran 1 test in 0.014s -135: -135: OK 136: file test5_1.png gave hash 1284534124U not the expected 2116545562U 136: file test5_2.png gave hash 1548238783U not the expected 1519942634U -124: [19:37:12] UFFTYPER: Warning: hybridization set to SP3 for atom 6 136: file test5_3.png gave hash 2001032737U not the expected 3266389887U 136: Done 136: ----------------- Test 6 (atom labels) -121/208 Test #135: pyMolCatalog ........................... Passed 0.28 sec -test 137 - Start 137: moldraw2DTestCatch - -137: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -137: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D -137: Test timeout computed to be: 1500 136: Done 136: ----------------- Test 7 (backgrounds) 136: file test7_1.png gave hash 2952006174U not the expected 3331950391U -97: =>start test 1 WHIM custom -97: [19:37:12] test on : 365 molecules done 136: file test7_2.png gave hash 425772459U not the expected 1686496331U 136: Done 136: ----------------- Test8: PrepareMolDrawing 136: Done 136: ----------------- Test multi-threaded drawing 136: reading molecules -118: [19:37:12] done -118: [19:37:12] ------------------------------------- -118: [19:37:12] Test MMFF multithreading2 -124: [19:37:12] UFFTYPER: Warning: hybridization set to SP3 for atom 6 136: generating reference drawings +136: processing +136: launch :0 +136: launch :1 +136: launch :2 +136: launch :3 +125: [16:03:26] Molecule does not have explicit Hs. Consider calling AddHs() +29: [16:03:26] Finished +29: [16:03:26] ------------------------------------- +29: [16:03:26] Test github1843: RWMol.clear() should not destroy ring pointer. +29: [16:03:26] Finished +130/208 Test #29: graphmolTest1 .......................... Passed 33.43 sec +test 137 + Start 137: moldraw2DTestCatch + +137: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +137: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D +137: Test timeout computed to be: 1500 137: file testAtomTags_3.svg gave hash 1231086273U not the expected 2131854465U -61: [19:37:13] Finished: testSDCorrectness() -61: [19:37:13] ----------------------------------------- -61: -122/208 Test #61: testMultithreadedMolSupplier ........... Passed 7.35 sec +125: [16:03:27] Molecule does not have explicit Hs. Consider calling AddHs() +137: file contourMol_1.svg gave hash 2981038842U not the expected 3218870758U +137: file contourMol_4.svg gave hash 2421490944U not the expected 764999893U +137: file testGithub3226_1.png gave hash 2295950490U not the expected 284815097U +137: file testGithub3226_2.png gave hash 3002722972U not the expected 2460913971U +137: file testGithub3226_3.png gave hash 2190299399U not the expected 993799198U +137: file testPNGMetadata_1.png gave hash 602868208U not the expected 2022143293U +137: file testPNGMetadata_2.png gave hash 868131113U not the expected 3078435362U +137: [16:03:27] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [16:03:27] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: file testHandDrawn-1.svg gave hash 2084647188U not the expected 799391905U +137: [16:03:27] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [16:03:27] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +125: [16:03:27] Molecule does not have explicit Hs. Consider calling AddHs() +123: validating reference data +137: file testHandDrawn-1.png gave hash 2911242399U not the expected 1551605661U +137: [16:03:27] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [16:03:27] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: file testHandDrawn-2.svg gave hash 413377600U not the expected 2605087576U +137: [16:03:27] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [16:03:27] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: file testHandDrawn-2.png gave hash 5059236U not the expected 2979412913U +137: [16:03:27] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [16:03:27] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: file testHandDrawn-3.svg gave hash 3544722771U not the expected 1015633173U +137: [16:03:27] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [16:03:27] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: file testHandDrawn-3.png gave hash 1399046867U not the expected 1765396301U +137: [16:03:27] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [16:03:27] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: file testHandDrawn-4.svg gave hash 3560563042U not the expected 830784921U +137: [16:03:27] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [16:03:27] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: file testHandDrawn-4.png gave hash 3343276360U not the expected 2989933219U +125: [16:03:27] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:28] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:03:28] Molecule does not have explicit Hs. Consider calling AddHs() +137: file testHandDrawn-5a.svg gave hash 3548322739U not the expected 2845825621U +137: [16:03:29] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [16:03:29] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: file testHandDrawn-5b.svg gave hash 2628549408U not the expected 476521352U +137: [16:03:29] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [16:03:29] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: file testHandDrawn-5.png gave hash 758356096U not the expected 1526220279U +137: file testBrackets-5a.svg gave hash 3194644554U not the expected 1388227932U +137: file testSGroupData-2b.svg gave hash 3713335027U not the expected 2573013307U +137: file testPositionVariation-1b.svg gave hash 544742604U not the expected 2588110577U +137: file testNoAtomLabels-2.svg gave hash 4051528137U not the expected 3213096674U +137: file testQueryBonds-1c.svg gave hash 1784325271U not the expected 333519907U +127: *********************************************************** +127: Testing O3AAlign +127: --------------------------------- +127: testMMFFO3A +127: +127: --------------------------------- +127: testMMFFO3A with pre-computed dmat and MolHistogram +127: +127: --------------------------------- +127: testMMFFO3A with constraints +127: +127: --------------------------------- +127: testMMFFO3A with variable weight constraints followed by local-only optimization +127: +127: --------------------------------- +127: testCrippenO3A +127: +127: --------------------------------- +127: testCrippenO3A with pre-computed dmat and MolHistogram +127: +127: --------------------------------- +127: testCrippenO3A with constraints +127: +127: --------------------------------- +127: testCrippenO3A with variable weight constraints followed by local-only optimization +127: +127: --------------------------------- +127: testMMFFO3A multithreading +127: +127: generating reference data +137: [16:03:29] unrecognized bond typefile testGithub4238_1.png gave hash 1493533853U not the expected 458925131U +137: file testGithub4323_1.svg gave hash 167590714U not the expected 1993234598U +137: file testGithub4323_1.png gave hash 858273747U not the expected 3711520691U +137: file testGithub4323_3.png gave hash 747920275U not the expected 2300228708U +137: [16:03:29] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. +137: file testDarkMode.1.svg gave hash 581654272U not the expected 1977391752U +137: file testMonochrome.1.svg gave hash 3944998716U not the expected 1776897420U +137: file testMonochrome.2.svg gave hash 3145122308U not the expected 399259780U +137: file testAvalon.1.svg gave hash 22748787U not the expected 1614166818U +137: file testCDK.1.svg gave hash 4152035316U not the expected 3108685638U +137: file testGithub4519_1.svg gave hash 4122076507U not the expected 473230604U +137: file testGithub4519_2.svg gave hash 2169321355U not the expected 2515716875U +137: file testGithub4519_4.svg gave hash 1879311203U not the expected 645908829U +137: file testBaseFontSize.1a.svg gave hash 4246301187U not the expected 3939288880U +125: .[16:03:29] Molecule does not have explicit Hs. Consider calling AddHs() +137: file testFlexiCanvas.2a.png gave hash 3596300350U not the expected 3618977786U +137: file testFlexiCanvas.2b.png gave hash 868015450U not the expected 2780757414U +137: file testFlexiCanvas.3.svg gave hash 1188140086U not the expected 1164132085U +137: file testGithub4764.sz1.svg gave hash 2429181530U not the expected 493786705U +137: file testGithub4764.sz2.svg gave hash 1556078230U not the expected 2704253898U +137: file testGithub4764.sz3.svg gave hash 1187691699U not the expected 1328896014U +137: file testGithub4764.sz1.png gave hash 2569031563U not the expected 2320783268U +137: file testGithub4764.sz2.png gave hash 3525848942U not the expected 3297570843U +137: file testGithub4764.sz3.png gave hash 2491935504U not the expected 2178018272U +137: file testDrawArc1.svg gave hash 305186657U not the expected 4039810147U +137: file testGithub_5269_1.svg gave hash 3635725957U not the expected 2368496794U +137: file testGithub_5269_2.svg gave hash 607835614U not the expected 567813292U +137: file github5383_1.png gave hash 93990453U not the expected 2963331215U +137: file github5156_2.svg gave hash 1130781980U not the expected 2606649270U +137: file github5156_3.svg gave hash 3982691065U not the expected 3284451122U +137: file acs1996_1.png gave hash 4036198339U not the expected 2674458798U +137: file acs1996_2.png gave hash 3786285444U not the expected 83755168U +137: file acs1996_4.svg gave hash 2040630632U not the expected 3372558370U +137: file acs1996_7.svg gave hash 2718384395U not the expected 763391533U +137: file acs1996_8.svg gave hash 1449819718U not the expected 939325262U +137: file acs1996_11.svg gave hash 4001805189U not the expected 2121789178U +137: [16:03:30] 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. +137: file bond_highlights_4.svg gave hash 2068128924U not the expected 4115973245U +137: file bond_highlights_8.svg gave hash 1796268304U not the expected 3826056528U +137: =============================================================================== +137: All tests passed (379 assertions in 67 test cases) +137: +131/208 Test #137: moldraw2DTestCatch ..................... Passed 3.57 sec test 138 Start 138: moldraw2DRxnTest1 138: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 138: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D 138: Test timeout computed to be: 1500 -137: file contourMol_1.svg gave hash 2981038842U not the expected 3218870758U 138: ----------------- Test 1 -124: [19:37:13] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -124: [19:37:13] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -137: file contourMol_4.svg gave hash 2421490944U not the expected 764999893U -136: processing -136: launch :0 -136: launch :1 -136: launch :2 -136: launch :3 -124: [19:37:13] UFFTYPER: Warning: hybridization set to SP3 for atom 11 138: file rxn_test1_1.png gave hash 410482668U not the expected 3579100589U -137: file testGithub3226_1.png gave hash 2295950490U not the expected 284815097U -124: =============================================================================== -124: All tests passed (163 assertions in 5 test cases) -124: -137: file testGithub3226_2.png gave hash 3002722972U not the expected 2460913971U -123/208 Test #124: distGeomHelpersCatch ................... Passed 2.68 sec -test 139 - Start 139: pyMolDraw2D - -139: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" -139: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap -139: Test timeout computed to be: 1500 -137: file testGithub3226_3.png gave hash 2190299399U not the expected 993799198U 138: file rxn_test1_2.png gave hash 3429731987U not the expected 3996724834U -137: file testPNGMetadata_1.png gave hash 602868208U not the expected 2022143293U 138: file rxn_test1_3.png gave hash 645713784U not the expected 4153817948U -137: file testPNGMetadata_2.png gave hash 868131113U not the expected 3078435362U -120: [19:37:13] done -120: [19:37:13] ------------------------------------- -120: [19:37:13] Test UFF multithreading2 138: file rxn_test1_4.png gave hash 1948425776U not the expected 4175225545U 138: file rxn_test1_5.png gave hash 918625681U not the expected 3400977230U -137: [19:37:13] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [19:37:13] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. -137: file testHandDrawn-1.svg gave hash 2084647188U not the expected 799391905U -137: [19:37:13] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [19:37:13] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 138: file rxn_test1_6.png gave hash 4273051481U not the expected 2636974466U 138: file rxn_test1_6.svg gave hash 3449991512U not the expected 3282888040U -137: file testHandDrawn-1.png gave hash 2911242399U not the expected 1551605661U 138: file rxn_test1_7.png gave hash 3500778798U not the expected 4164917700U 138: file rxn_test1_7.svg gave hash 3991517232U not the expected 1748644916U 138: Done 138: ----------------- Test 2: some examples that caused problems in testing 138: file rxn_test2_1.png gave hash 2789407966U not the expected 2654417911U -137: [19:37:13] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [19:37:13] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 138: 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 -137: file testHandDrawn-2.svg gave hash 413377600U not the expected 2605087576U -137: [19:37:13] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [19:37:13] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 138: file rxn_test2_2_1.png gave hash 2636323184U not the expected 997060634U 138: 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 -137: file testHandDrawn-2.png gave hash 5059236U not the expected 2979412913U -137: [19:37:13] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [19:37:13] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 138: file rxn_test2_2_2.png gave hash 3205071265U not the expected 2090979640U -118: [19:37:13] done -118: [19:37:13] ------------------------------------- -118: [19:37:13] Test MMFF multithreading3 -137: file testHandDrawn-3.svg gave hash 3544722771U not the expected 1015633173U -137: [19:37:13] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [19:37:13] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 138: 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 138: 2 C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl 138: 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 -137: file testHandDrawn-3.png gave hash 1399046867U not the expected 1765396301U 138: file rxn_test2_2_3.png gave hash 3292764551U not the expected 857100114U -137: [19:37:13] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [19:37:13] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. -137: file testHandDrawn-4.svg gave hash 3560563042U not the expected 830784921U -137: [19:37:13] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [19:37:13] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 138: 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 138: file rxn_test2_2_4.png gave hash 2890404885U not the expected 610638635U -137: file testHandDrawn-4.png gave hash 3343276360U not the expected 2989933219U 138: Done 138: ----------------- Test 3: test reactant highlighting +123: processing +123: launch :0 +123: launch :1 +123: launch :2 +123: launch :3 138: file rxn_test3_1.png gave hash 1974828383U not the expected 501226401U -139: ...[19:37:13] Font file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. -139: [19:37:13] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 138: file rxn_test3_1.svg gave hash 582901546U not the expected 3321754513U 138: Done 138: ----------------- Test 4: some examples from SMARTS in testing 138: draw! -139: ..........[19:37:14] +138: file rxn_test4_1.png gave hash 3256430128U not the expected 805353504U +138: file rxn_test4_1.svg gave hash 1178703228U not the expected 1987969092U +138: done +138: file rxn_test4_2.png gave hash 555777641U not the expected 2842629749U +138: file rxn_test4_2.svg gave hash 1024639429U not the expected 946039978U +138: Done +132/208 Test #138: moldraw2DRxnTest1 ...................... Passed 0.55 sec +test 139 + Start 139: pyMolDraw2D + +139: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" +139: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap +139: Test timeout computed to be: 1500 +127: processing +127: launch :0 +127: launch :1 +127: launch :2 +127: launch :3 +139: ...[16:03:31] Font file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. +139: [16:03:31] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +139: ..........[16:03:31] 139: 139: **** 139: Pre-condition Violation @@ -24494,45 +24819,670 @@ 139: Failed Expression: m 139: **** 139: -138: file rxn_test4_1.png gave hash 3256430128U not the expected 805353504U -138: file rxn_test4_1.svg gave hash 1178703228U not the expected 1987969092U -138: done -120: [19:37:14] done -120: [19:37:14] ------------------------------------- -120: [19:37:14] Test UFF multithreading3 -138: file rxn_test4_2.png gave hash 555777641U not the expected 2842629749U -138: file rxn_test4_2.svg gave hash 1024639429U not the expected 946039978U -138: Done -124/208 Test #138: moldraw2DRxnTest1 ...................... Passed 1.32 sec +139: ................... +139: ---------------------------------------------------------------------- +139: Ran 32 tests in 0.630s +139: +139: OK +133/208 Test #139: pyMolDraw2D ............................ Passed 1.28 sec test 140 Start 140: testFMCS 140: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/testFMCS 140: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS 140: Test timeout computed to be: 1500 -123: building molecules -125: [19:37:14] Molecule does not have explicit Hs. Consider calling AddHs() -139: ................... -139: ---------------------------------------------------------------------- -139: Ran 32 tests in 0.809s -139: -139: OK -118: [19:37:14] done -118: [19:37:14] ------------------------------------- -118: [19:37:14] Testing github 162: Incorrect SMILES after MMFF parameterization . -118: [19:37:14] done -118: [19:37:14] ------------------------------------- -118: [19:37:14] Testing github 224: crash during MMFF parameterization . -118: [19:37:14] done -123: generating reference data -125/208 Test #118: testMMFFForceFieldHelpers .............. Passed 4.78 sec +136: Done +136: ----------------- Test Github #781: Rendering single-atom molecules +136: file testGithub781_3.svg gave hash 4141108304U not the expected 3655151266U +136: Done +136: ----------------- Test 3 +136: file test3_1.png gave hash 457962218U not the expected 1578780280U +136: file test3_2.png gave hash 3723407046U not the expected 1100583374U +136: file test3_3.png gave hash 715516981U not the expected 2405974883U +136: file test3_3.svg gave hash 220863844U not the expected 3967096277U +136: file test3_4.png gave hash 2817418133U not the expected 3523404550U +136: file test3_4.svg gave hash 2724848547U not the expected 1410409071U +136: file test3_5.png gave hash 2019575530U not the expected 411486117U +136: file test3_6.png gave hash 946969094U not the expected 2817453573U +136: file test3_7.png gave hash 1623443833U not the expected 285272009U +136: Done +136: ----------------- Test Github774: upside-down drawings +136: file test774_1.png gave hash 3501940912U not the expected 930347428U +136: file test774_2.png gave hash 3395890193U not the expected 1089219024U +136: Done +136: ----------------- Test 9 (molecule legends) +136: file test9_1.svg gave hash 618149026U not the expected 3204904541U +136: Done +136: ----------------- Test Github852: Lines used to wedge bonds are too thick +136: file test852_1.png gave hash 171258688U not the expected 4140960740U +136: file test852_2.png gave hash 3927167691U not the expected 4294133823U +136: ---------------- +136: ---------------- +136: ---------------- +136: ---------------- +136: Done +136: ----------------- Test Github860: Atom symbols in wrong order if bond comes from right +136: file test860_1.png gave hash 2949617705U not the expected 1000110983U +136: file test860_2.png gave hash 1584078969U not the expected 4079976606U +136: file test860_3.png gave hash 3063101059U not the expected 1675954369U +136: Done +136: ----------------- Test Github #910: ugly coordinates generated for peptide chains +136: Done +136: ----------------- Test Github #932: mistake in SVG for wedged bonds +136: Done +136: ----------------- Test Github #953: default color should not be cyan +136: Done +136: ----------------- Test Github #983: wedged bonds between chiral centers drawn improperly +136: Done +136: ----------------- Test Deuterium, Tritium +136: Done +136: ----------------- Test crossed bonds +136: Done +136: ----------------- Testing drawing a second molecule +136: Done +136: ----------------- Testing drawing a grid of molecules +136: Done +136: ----------------- Testing drawMolecules +136: file test12_1.svg gave hash 2818547989U not the expected 459314393U +136: file test12_5.svg gave hash 816880708U not the expected 3040108534U +136: Done +136: ----------------- Test JSON Configuration +136: Done +136: ----------------- Testing github 1090: escape html characters in SVG output +140: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds +140: Time elapsed 0.000 seconds +140: +140: test32() +140: 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 +140: Time elapsed 0.176 seconds +140: +140: test190() +140: 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 +140: Time elapsed 0.020 seconds +140: +140: test3() +140: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds +140: Time elapsed 0.034 seconds +140: +140: testSimpleFast() +140: 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 +140: Time elapsed 0.304 seconds +140: +140: testSimple() +140: MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds +140: Time elapsed 0.317 seconds +140: MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds +140: Time elapsed 0.335 seconds +140: MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds +140: Time elapsed 0.344 seconds +140: +140: testSegFault() +140: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds +140: Time elapsed 0.029 seconds +140: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds +140: Time elapsed 0.022 seconds +140: MCS MatchFusedRingsStrict: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds +140: Time elapsed 0.032 seconds +140: +140: testThreshold() +140: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +140: Time elapsed 0.000 seconds +140: +140: testRing1() +140: 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 +140: Time elapsed 1.306 seconds +140: 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 +140: Time elapsed 0.428 seconds +140: MCS MatchFusedRingsStrict: [#6]1:&@[#6]:&@[#7]:&@[#6](:&@[#6]:&@[#6]:&@1)-&!@[#6](=&!@[#8])-&!@[#8]-&!@[#6](-&!@[#6])-&!@[#6] 12 atoms, 12 bonds +140: Time elapsed 0.380 seconds +140: +140: testAtomCompareIsotopes() +140: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds +140: Time elapsed 0.005 seconds +140: +140: testAtomCompareAnyAtom() +140: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds +140: Time elapsed 0.000 seconds +140: +140: testAtomCompareAnyAtom() +140: MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds +140: Time elapsed 0.000 seconds +140: +140: testAtomCompareAnyAtom() +140: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds +140: Time elapsed 0.000 seconds +140: +140: testAtomCompareAnyAtom() +140: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds +140: Time elapsed 0.000 seconds +140: +140: testJnk1LigandsDistance() +140: 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 +140: Time elapsed 0.030 seconds +140: 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 +136: Done +136: ----------------- Testing github 1035: overflow bug in SVG color generation +136: Done +136: ----------------- Testing github 1271: MolDraw2D not drawing anything for molecules aligned with the X or Y axes +136: Done +136: ----------------- Testing github 1322: add custom atom labels +136: Done +136: ----------------- Testing use of a black & white palette +136: Done +136: ----------------- Testing use of continuous highlighting with drawMolecules +136: Done +136: ----------------- Test 17 - Testing maximum font size +136: Done +136: ----------------- Testing github 1829: crash when drawMolecules() is called with an empty list +136: Done +136: ----------------- Testing use of fixed scales for drawing. +136: file test18_5.svg gave hash 548307340U not the expected 3983014844U +136: [16:03:36] +136: +136: **** +136: Test Assert +136: Expression Failed: +136: Violation occurred on line 3392 in file ./Code/GraphMol/MolDraw2D/test1.cpp +136: Failed Expression: drawer.fontSize() == 24 +136: **** +136: +136: terminate called after throwing an instance of 'Invar::Invariant' +136: what(): Expression Failed: +134/208 Test #136: moldraw2DTest1 .........................Subprocess aborted***Exception: 10.73 sec + ----------------- Test 1 +file test1_5.svg gave hash 3105787089U not the expected 2964125114U +file test1_6.svg gave hash 995867455U not the expected 464012122U + Done + ----------------- Test 2 +file test2_1.png gave hash 2637189532U not the expected 2505713963U +file test2_2.png gave hash 2877988061U not the expected 4058920248U + Done + ----------------- Test 4 +file test4_1.png gave hash 747479389U not the expected 1924202631U + Done + ----------------- Test 5 +file test5_1.png gave hash 1284534124U not the expected 2116545562U +file test5_2.png gave hash 1548238783U not the expected 1519942634U +file test5_3.png gave hash 2001032737U not the expected 3266389887U + Done + ----------------- Test 6 (atom labels) + Done + ----------------- Test 7 (backgrounds) +file test7_1.png gave hash 2952006174U not the expected 3331950391U +file test7_2.png gave hash 425772459U not the expected 1686496331U + Done + ----------------- Test8: PrepareMolDrawing + Done + ----------------- Test multi-threaded drawing +reading molecules +generating reference drawings +processing + launch :0 + launch :1 + launch :2 + launch :3 + Done + ----------------- Test Github #781: Rendering single-atom molecules +file testGithub781_3.svg gave hash 4141108304U not the expected 3655151266U + Done + ----------------- Test 3 +file test3_1.png gave hash 457962218U not the expected 1578780280U +file test3_2.png gave hash 3723407046U not the expected 1100583374U +file test3_3.png gave hash 715516981U not the expected 2405974883U +file test3_3.svg gave hash 220863844U not the expected 3967096277U +file test3_4.png gave hash 2817418133U not the expected 3523404550U +file test3_4.svg gave hash 2724848547U not the expected 1410409071U +file test3_5.png gave hash 2019575530U not the expected 411486117U +file test3_6.png gave hash 946969094U not the expected 2817453573U +file test3_7.png gave hash 1623443833U not the expected 285272009U + Done + ----------------- Test Github774: upside-down drawings +file test774_1.png gave hash 3501940912U not the expected 930347428U +file test774_2.png gave hash 3395890193U not the expected 1089219024U + Done + ----------------- Test 9 (molecule legends) +file test9_1.svg gave hash 618149026U not the expected 3204904541U + Done + ----------------- Test Github852: Lines used to wedge bonds are too thick +file test852_1.png gave hash 171258688U not the expected 4140960740U +file test852_2.png gave hash 3927167691U not the expected 4294133823U +---------------- +---------------- +---------------- +---------------- + Done + ----------------- Test Github860: Atom symbols in wrong order if bond comes from right +file test860_1.png gave hash 2949617705U not the expected 1000110983U +file test860_2.png gave hash 1584078969U not the expected 4079976606U +file test860_3.png gave hash 3063101059U not the expected 1675954369U + Done + ----------------- Test Github #910: ugly coordinates generated for peptide chains + Done + ----------------- Test Github #932: mistake in SVG for wedged bonds + Done + ----------------- Test Github #953: default color should not be cyan + Done + ----------------- Test Github #983: wedged bonds between chiral centers drawn improperly + Done + ----------------- Test Deuterium, Tritium + Done + ----------------- Test crossed bonds + Done + ----------------- Testing drawing a second molecule + Done + ----------------- Testing drawing a grid of molecules + Done + ----------------- Testing drawMolecules +file test12_1.svg gave hash 2818547989U not the expected 459314393U +file test12_5.svg gave hash 816880708U not the expected 3040108534U + Done + ----------------- Test JSON Configuration + Done + ----------------- Testing github 1090: escape html characters in SVG output + Done + ----------------- Testing github 1035: overflow bug in SVG color generation + Done + ----------------- Testing github 1271: MolDraw2D not drawing anything for molecules aligned with the X or Y axes + Done + ----------------- Testing github 1322: add custom atom labels + Done + ----------------- Testing use of a black & white palette + Done + ----------------- Testing use of continuous highlighting with drawMolecules + Done + ----------------- Test 17 - Testing maximum font size + Done + ----------------- Testing github 1829: crash when drawMolecules() is called with an empty list + Done + ----------------- Testing use of fixed scales for drawing. +file test18_5.svg gave hash 548307340U not the expected 3983014844U +[16:03:36] + +**** +Test Assert +Expression Failed: +Violation occurred on line 3392 in file ./Code/GraphMol/MolDraw2D/test1.cpp +Failed Expression: drawer.fontSize() == 24 +**** + +terminate called after throwing an instance of 'Invar::Invariant' + what(): Expression Failed: + test 141 Start 141: pyFMCS 141: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Wrap/testFMCS.py" 141: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Wrap 141: Test timeout computed to be: 1500 -126/208 Test #139: pyMolDraw2D ............................ Passed 1.58 sec +140: Time elapsed 0.002 seconds +140: +140: test18() +140: 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 +140: 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 +140: Time elapsed 0.023 seconds +140: +140: test504() +140: 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 +140: 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 +140: Time elapsed 0.280 seconds +140: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds +140: Time elapsed 0.006 seconds +140: 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 +140: Time elapsed 0.082 seconds +140: Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds +140: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0054 seconds. bond[0]=6 +140: STATISTICS: +140: Total Growing Steps = 1, MCS found on 1 step, for 0.0054 seconds +140: Initial Seeds = 1, Mismatched 0 +140: Inspected Seeds = 2 +140: Rejected by BestSize = 0 +140: SingleBondExcluded = 0 +140: MatchCheck Seeds = 2 +140: MatchCalls = 2 +140: MatchFound = 1 +140: fastMatchCalls = 1 +140: fastMatchFound = 0 +140: slowMatchCalls = 2 +140: slowMatchFound = 1 +140: DupCacheFound = 0 0 matched, 0 mismatched +140: HashCache size = 1 keys +140: HashCache size = 1 entries +140: FindHashInCache = 2 +140: HashFoundInCache= 0 +140: ExactMatchCalls = 0 +140: ExactMatchFound = 0 +140: Time elapsed 0.006 seconds +140: query=OCCl SubstructMatch(useChirality=false) res =1 size=3 +140: query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 +140: test target = O[C@H](F)CCl query = C(F)C useChirality = 0 +140: res sub = 1 size=3 +140: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds +140: test target = O[C@H](F)CCl query = C(F)C useChirality = 1 +140: res sub = 1 size=3 +140: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds +140: test target = CC[C@H](F)Cl query = CCC useChirality = 0 +140: res sub = 1 size=3 +140: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +140: test target = CC[C@H](F)Cl query = CCC useChirality = 1 +140: res sub = 1 size=3 +140: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +140: test target = CCC(F)Cl query = CC useChirality = 0 +140: res sub = 1 size=2 +140: MCS: [#6]-[#6] 2 atoms, 1 bonds +140: test target = CCC(F)Cl query = CC useChirality = 1 +140: res sub = 1 size=2 +140: MCS: [#6]-[#6] 2 atoms, 1 bonds +140: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 0 +140: res sub = 1 size=4 +140: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +140: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 1 +140: res sub = 1 size=4 +140: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +140: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 0 +140: res sub = 1 size=4 +140: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +140: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 1 +140: res sub = 1 size=4 +140: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +140: test target = O[C@H](F)CCl query = CC(F)C useChirality = 0 +140: res sub = 0 size=0 +140: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds +140: test target = O[C@H](F)CCl query = CC(F)C useChirality = 1 +140: res sub = 0 size=0 +140: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds +140: test target = O[C@H](F)CCl query = OC(F)C useChirality = 0 +140: res sub = 1 size=4 +140: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +140: test target = O[C@H](F)CCl query = OC(F)C useChirality = 1 +140: res sub = 1 size=4 +140: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +140: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 0 +140: res sub = 1 size=4 +140: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +140: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 1 +140: res sub = 1 size=4 +140: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +140: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 0 +140: res sub = 1 size=4 +140: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +140: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 1 +140: res sub = 0 size=0 +140: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +140: test target = OC(F)CCl query = OC(F)C useChirality = 0 +140: res sub = 1 size=4 +140: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +140: test target = OC(F)CCl query = OC(F)C useChirality = 1 +140: res sub = 1 size=4 +140: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +140: test target = OC(F)CCl query = O[C@H](F)C useChirality = 0 +140: res sub = 1 size=4 +140: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +140: test target = OC(F)CCl query = O[C@H](F)C useChirality = 1 +140: res sub = 0 size=0 +140: MCS: [#9] 1 atoms, 0 bonds +140: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 0 +140: res sub = 1 size=4 +140: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +140: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 1 +140: res sub = 0 size=0 +140: MCS: [#9] 1 atoms, 0 bonds +140: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 0 +140: res sub = 1 size=3 +140: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +140: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 1 +140: res sub = 1 size=3 +140: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +140: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 0 +140: res sub = 1 size=3 +140: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +140: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 1 +140: res sub = 1 size=3 +140: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +140: +140: 0. <<<<<<<<< actual MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds >>>>>>> +140: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 0 +140: res sub = 1 size=3 +140: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +140: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 1 +140: res sub = 1 size=3 +140: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +140: done +140: MCS: [#6]1-&@[#6](-&!@[#6])-&@[#6]-&@[#6]-&@[#6]-&@[#6]-&@1 7 atoms, 7 bonds +140: +140: MCS: [#6]-&!@[#6] 2 atoms, 1 bonds +140: +140: [16:03:37] +140: +140: **** +140: Test Assert +140: Expression Failed: +140: Violation occurred on line 2326 in file ./Code/GraphMol/FMCS/testFMCS_Unit.cpp +140: Failed Expression: res.NumAtoms == 17 +140: **** +140: +140: terminate called after throwing an instance of 'Invar::Invariant' +140: what(): Expression Failed: +135/208 Test #140: testFMCS ...............................Subprocess aborted***Exception: 4.98 sec +MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds +Time elapsed 0.000 seconds + + test32() +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 +Time elapsed 0.176 seconds + + test190() +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 +Time elapsed 0.020 seconds + + test3() +MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds +Time elapsed 0.034 seconds + +testSimpleFast() +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 +Time elapsed 0.304 seconds + +testSimple() +MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds +Time elapsed 0.317 seconds +MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds +Time elapsed 0.335 seconds +MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds +Time elapsed 0.344 seconds + +testSegFault() +MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds +Time elapsed 0.029 seconds +MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds +Time elapsed 0.022 seconds +MCS MatchFusedRingsStrict: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds +Time elapsed 0.032 seconds + +testThreshold() +MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +Time elapsed 0.000 seconds + +testRing1() +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 +Time elapsed 1.306 seconds +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 +Time elapsed 0.428 seconds +MCS MatchFusedRingsStrict: [#6]1:&@[#6]:&@[#7]:&@[#6](:&@[#6]:&@[#6]:&@1)-&!@[#6](=&!@[#8])-&!@[#8]-&!@[#6](-&!@[#6])-&!@[#6] 12 atoms, 12 bonds +Time elapsed 0.380 seconds + +testAtomCompareIsotopes() +MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds +Time elapsed 0.005 seconds + +testAtomCompareAnyAtom() +MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds +Time elapsed 0.000 seconds + +testAtomCompareAnyAtom() +MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds +Time elapsed 0.000 seconds + +testAtomCompareAnyAtom() +MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds +Time elapsed 0.000 seconds + +testAtomCompareAnyAtom() +MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds +Time elapsed 0.000 seconds + +testJnk1LigandsDistance() +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 +Time elapsed 0.030 seconds +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 +Time elapsed 0.002 seconds + +test18() +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 +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 +Time elapsed 0.023 seconds + +test504() +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 +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 +Time elapsed 0.280 seconds +MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds +Time elapsed 0.006 seconds +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 +Time elapsed 0.082 seconds +Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds +1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0054 seconds. bond[0]=6 +STATISTICS: +Total Growing Steps = 1, MCS found on 1 step, for 0.0054 seconds +Initial Seeds = 1, Mismatched 0 +Inspected Seeds = 2 +Rejected by BestSize = 0 +SingleBondExcluded = 0 +MatchCheck Seeds = 2 + MatchCalls = 2 + MatchFound = 1 + fastMatchCalls = 1 + fastMatchFound = 0 + slowMatchCalls = 2 + slowMatchFound = 1 + DupCacheFound = 0 0 matched, 0 mismatched +HashCache size = 1 keys +HashCache size = 1 entries +FindHashInCache = 2 +HashFoundInCache= 0 +ExactMatchCalls = 0 +ExactMatchFound = 0 +Time elapsed 0.006 seconds +query=OCCl SubstructMatch(useChirality=false) res =1 size=3 +query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 +test target = O[C@H](F)CCl query = C(F)C useChirality = 0 +res sub = 1 size=3 +MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds +test target = O[C@H](F)CCl query = C(F)C useChirality = 1 +res sub = 1 size=3 +MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds +test target = CC[C@H](F)Cl query = CCC useChirality = 0 +res sub = 1 size=3 +MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +test target = CC[C@H](F)Cl query = CCC useChirality = 1 +res sub = 1 size=3 +MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +test target = CCC(F)Cl query = CC useChirality = 0 +res sub = 1 size=2 +MCS: [#6]-[#6] 2 atoms, 1 bonds +test target = CCC(F)Cl query = CC useChirality = 1 +res sub = 1 size=2 +MCS: [#6]-[#6] 2 atoms, 1 bonds +test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 0 +res sub = 1 size=4 +MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 1 +res sub = 1 size=4 +MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 0 +res sub = 1 size=4 +MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 1 +res sub = 1 size=4 +MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +test target = O[C@H](F)CCl query = CC(F)C useChirality = 0 +res sub = 0 size=0 +MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds +test target = O[C@H](F)CCl query = CC(F)C useChirality = 1 +res sub = 0 size=0 +MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds +test target = O[C@H](F)CCl query = OC(F)C useChirality = 0 +res sub = 1 size=4 +MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +test target = O[C@H](F)CCl query = OC(F)C useChirality = 1 +res sub = 1 size=4 +MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 0 +res sub = 1 size=4 +MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 1 +res sub = 1 size=4 +MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 0 +res sub = 1 size=4 +MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 1 +res sub = 0 size=0 +MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +test target = OC(F)CCl query = OC(F)C useChirality = 0 +res sub = 1 size=4 +MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +test target = OC(F)CCl query = OC(F)C useChirality = 1 +res sub = 1 size=4 +MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +test target = OC(F)CCl query = O[C@H](F)C useChirality = 0 +res sub = 1 size=4 +MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +test target = OC(F)CCl query = O[C@H](F)C useChirality = 1 +res sub = 0 size=0 +MCS: [#9] 1 atoms, 0 bonds +test target = OC(F)CCl query = O[C@@H](F)C useChirality = 0 +res sub = 1 size=4 +MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +test target = OC(F)CCl query = O[C@@H](F)C useChirality = 1 +res sub = 0 size=0 +MCS: [#9] 1 atoms, 0 bonds +test target = O[C@H](F)CCl query = O[C@H]C useChirality = 0 +res sub = 1 size=3 +MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +test target = O[C@H](F)CCl query = O[C@H]C useChirality = 1 +res sub = 1 size=3 +MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 0 +res sub = 1 size=3 +MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 1 +res sub = 1 size=3 +MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds + +0. <<<<<<<<< actual MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds >>>>>>> +test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 0 +res sub = 1 size=3 +MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 1 +res sub = 1 size=3 +MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds + done +MCS: [#6]1-&@[#6](-&!@[#6])-&@[#6]-&@[#6]-&@[#6]-&@[#6]-&@1 7 atoms, 7 bonds + +MCS: [#6]-&!@[#6] 2 atoms, 1 bonds + +[16:03:37] + +**** +Test Assert +Expression Failed: +Violation occurred on line 2326 in file ./Code/GraphMol/FMCS/testFMCS_Unit.cpp +Failed Expression: res.NumAtoms == 17 +**** + +terminate called after throwing an instance of 'Invar::Invariant' + what(): Expression Failed: + test 142 Start 142: FMCStest @@ -26504,69 +27454,38 @@ 142: 142: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 142: ERROR: RDKit could not load input file -127/208 Test #142: FMCStest ............................... Passed 0.23 sec +136/208 Test #142: FMCStest ............................... Passed 0.12 sec test 143 Start 143: molHashCatchTest 143: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest 143: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolHash 143: Test timeout computed to be: 1500 -120: [19:37:15] done -120: [19:37:15] ------------------------------------- -120: [19:37:15] Testing GitHubIssue62. -120: [19:37:15] beta-lactam 39.6387 -120: [19:37:15] cyclopropanone 174.698 -120: [19:37:15] aziridine 337.986 -120: [19:37:15] aziridinone 115.248 -120: [19:37:15] isobutene 2.48217 -125: [19:37:15] Molecule does not have explicit Hs. Consider calling AddHs() -120: [19:37:15] acetone 1.91788 -120: [19:37:15] cyclopentanone 10.1648 -120: [19:37:15] cyclopropene 99.4921 -120: [19:37:15] cyclobutene 41.0156 -120: [19:37:15] cyclopropane 267.236 -120: [19:37:15] gamma-lactam 15.7471 143: =============================================================================== 143: All tests passed (60 assertions in 5 test cases) 143: -128/208 Test #143: molHashCatchTest ....................... Passed 0.07 sec +137/208 Test #143: molHashCatchTest ....................... Passed 0.10 sec test 144 Start 144: pyMolHash 144: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/Wrap/testMolHash.py" 144: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolHash/Wrap 144: Test timeout computed to be: 1500 -120: [19:37:15] trans-2,3-diphenylcyclopropan-1-one 203.398 -120: [19:37:15] cis-2,3-diphenylcyclopropan-1-one 206.852 -120: [19:37:15] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 -120: [19:37:15] cyclopropylidencyclobutane 218.879 -120: [19:37:15] diphenylmethylidencyclobutane 79.6139 -120: [19:37:15] done -120: [19:37:15] ------------------------------------- -120: [19:37:15] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. -120: [19:37:15] done -120: [19:37:15] ------------------------------------- -120: [19:37:15] Test square planar complexes -120: [19:37:15] done -120: [19:37:15] ------------------------------------- -120: [19:37:15] Test octahedral complexes -120: [19:37:15] done -129/208 Test #120: testUFFForceFieldHelpers ............... Passed 5.18 sec +144: .. +144: ---------------------------------------------------------------------- +144: Ran 2 tests in 0.034s +144: +144: OK +138/208 Test #144: pyMolHash .............................. Passed 0.59 sec test 145 Start 145: testMMPA 145: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA/testMMPA 145: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA 145: Test timeout computed to be: 1500 -125: [19:37:15] Molecule does not have explicit Hs. Consider calling AddHs() -144: .. -144: ---------------------------------------------------------------------- -144: Ran 2 tests in 0.015s -144: -144: OK 145: 145: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -145: Time elapsed 0.005110 seconds +145: Time elapsed 0.009059 seconds 145: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 145: 1: NOREF. Reference data NOT LISTED in test case. 145: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 @@ -26581,13 +27500,6 @@ 145: 6: NOREF. Reference data NOT LISTED in test case. 145: 7: res= NULL,C[C:2](C(=O)N[*:1])[NH+]1CCCC1.Cc1ccccc1[*:1] 145: 7: NOREF. Reference data NOT LISTED in test case. -130/208 Test #144: pyMolHash .............................. Passed 0.30 sec -test 146 - Start 146: pyMMPA - -146: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/Wrap/testMMPA.py" -146: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap -146: Test timeout computed to be: 1500 145: 8: res= O=C(N[*:3])[*:1],C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1[*:3] 145: 8: NOREF. Reference data NOT LISTED in test case. 145: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2] @@ -26614,7 +27526,7 @@ 145: --- UNMATCHED Reference RESULTS: --- 145: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 145: ----------------------------------- -145: Time elapsed 0.004543 seconds +145: Time elapsed 0.012167 seconds 145: 145: TEST 1 mol: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 145: 1: NULL, C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O @@ -26656,7 +27568,7 @@ 145: ----------------------------------- 145: 145: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 -145: Time elapsed 0.004594 seconds +145: Time elapsed 0.004709 seconds 145: 1: res= NULL,C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 145: 1: PASSED. matchedRefRes = 4 145: 2: res= O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21,C[*:1].O=C(NCCO)[*:2] @@ -26696,7 +27608,7 @@ 145: ----------------------------------- 145: 145: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE -145: Time elapsed 0.001264 seconds +145: Time elapsed 0.001171 seconds 145: 1: res= NULL,C[*:1].O=CC(N1CC1)[*:1] 145: 1: PASSED. matchedRefRes = 2 145: 2: res= O=CC([*:1])[*:2],C1CN1[*:2].C[*:1] @@ -26718,7 +27630,7 @@ 145: ----------------------------------- 145: 145: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -145: Time elapsed 0.004829 seconds +145: Time elapsed 0.005569 seconds 145: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 145: 1: NOREF. Reference data NOT LISTED in test case. 145: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 @@ -26761,7 +27673,7 @@ 145: ----------------------------------- 145: 145: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 -145: Time elapsed 0.005422 seconds +145: Time elapsed 0.005250 seconds 145: 1: res= NULL,O=C(O[*:1])C(O)c1ccccc1.c1ccc(C[*:1])cc1 145: 1: NOREF. Reference data NOT LISTED in test case. 145: 2: res= C([*:1])[*:2],O=C(O[*:1])C(O)c1ccccc1.c1ccc([*:2])cc1 @@ -26802,161 +27714,101 @@ 145: --- ALL PASSED --- 145: ----------------------------------- 145: 5 TEST CASES FAILED -131/208 Test #145: testMMPA ............................... Passed 0.18 sec +139/208 Test #145: testMMPA ............................... Passed 0.22 sec +test 146 + Start 146: pyMMPA + +146: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/Wrap/testMMPA.py" +146: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap +146: Test timeout computed to be: 1500 +146: ......... +146: ---------------------------------------------------------------------- +146: Ran 9 tests in 2.097s +146: +146: OK +140/208 Test #146: pyMMPA ................................. Passed 2.63 sec test 147 Start 147: testCIPLabeler 147: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler 147: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler 147: Test timeout computed to be: 1500 -125: [19:37:15] Molecule does not have explicit Hs. Consider calling AddHs() -147: [19:37:15] non kekulizable aromatic bond being treated as bond order 1 -147: [19:37:15] non kekulizable aromatic bond being treated as bond order 1 -147: [19:37:15] non kekulizable aromatic bond being treated as bond order 1 -147: [19:37:15] non kekulizable aromatic bond being treated as bond order 1 -147: [19:37:15] non kekulizable aromatic bond being treated as bond order 1 -147: [19:37:15] non kekulizable aromatic bond being treated as bond order 1 +147: [16:03:41] non kekulizable aromatic bond being treated as bond order 1 +147: [16:03:41] non kekulizable aromatic bond being treated as bond order 1 +147: [16:03:41] non kekulizable aromatic bond being treated as bond order 1 +147: [16:03:41] non kekulizable aromatic bond being treated as bond order 1 +147: [16:03:41] non kekulizable aromatic bond being treated as bond order 1 +147: [16:03:41] non kekulizable aromatic bond being treated as bond order 1 147: =============================================================================== 147: All tests passed (5974 assertions in 12 test cases) 147: -132/208 Test #147: testCIPLabeler ......................... Passed 0.07 sec +141/208 Test #147: testCIPLabeler ......................... Passed 0.08 sec test 148 Start 148: pyCIPLabelsWrapTest 148: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py" 148: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 148: Test timeout computed to be: 1500 -137: file testHandDrawn-5a.svg gave hash 3548322739U not the expected 2845825621U -137: [19:37:15] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [19:37:15] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. -137: file testHandDrawn-5b.svg gave hash 2628549408U not the expected 476521352U -137: [19:37:15] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [19:37:15] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. -137: file testHandDrawn-5.png gave hash 758356096U not the expected 1526220279U +129: ............[16:03:41] Molecule does not have explicit Hs. Consider calling AddHs() 148: ... 148: ---------------------------------------------------------------------- -148: Ran 3 tests in 0.013s +148: Ran 3 tests in 0.016s 148: 148: OK -137: file testBrackets-5a.svg gave hash 3194644554U not the expected 1388227932U -133/208 Test #148: pyCIPLabelsWrapTest .................... Passed 0.28 sec +142/208 Test #148: pyCIPLabelsWrapTest .................... Passed 0.29 sec test 149 Start 149: pyCIPLabelsValidation 149: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py" 149: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 149: Test timeout computed to be: 1500 -125: [19:37:15] Molecule does not have explicit Hs. Consider calling AddHs() -137: file testSGroupData-2b.svg gave hash 3713335027U not the expected 2573013307U -137: file testPositionVariation-1b.svg gave hash 544742604U not the expected 2588110577U -137: file testNoAtomLabels-2.svg gave hash 4051528137U not the expected 3213096674U -137: file testQueryBonds-1c.svg gave hash 1784325271U not the expected 333519907U -137: [19:37:16] unrecognized bond typefile testGithub4238_1.png gave hash 1493533853U not the expected 458925131U -137: file testGithub4323_1.svg gave hash 167590714U not the expected 1993234598U -137: file testGithub4323_1.png gave hash 858273747U not the expected 3711520691U -108: [19:37:16] done -108: [19:37:16] ------------------------------------- -108: [19:37:16] Test GitHub Issue 258: Bad pattern fingerprint for query molecule -108: [19:37:16] done -108: [19:37:16] ------------------------------------- -108: [19:37:16] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -108: [19:37:16] done -108: [19:37:16] ------------------------------------- -108: [19:37:16] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -108: [19:37:16] done -108: [19:37:16] ------------------------------------- -108: [19:37:16] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -108: [19:37:16] Warning: molecule is tagged as 3D, but all Z coords are zero -108: [19:37:16] done -108: [19:37:16] ------------------------------------- -108: [19:37:16] Test unfolded version of RDKFP -108: [19:37:16] ------------------------------------- -108: [19:37:16] Test bitinfo of RDKFP -108: [19:37:16] ------------------------------------- -108: [19:37:16] Single atoms setting radius 1 bits in Morgan fingerprints -108: [19:37:16] done -108: [19:37:16] ------------------------------------- -108: [19:37:16] Github #879: Pattern fingerprint should set bits for single-atom fragments. -108: [19:37:16] done -108: [19:37:16] ------------------------------------- -108: [19:37:16] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms -108: [19:37:16] done -108: [19:37:16] ------------------------------------- -108: [19:37:16] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False -108: [19:37:16] done -108: [19:37:16] ------------------------------------- -108: [19:37:16] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called -108: [19:37:16] done -108: [19:37:16] ------------------------------------- -108: [19:37:16] Github #2115: BitInfo not complete for RDKFingerprint -108: [19:37:16] done -108: [19:37:16] ------------------------------------- -108: [19:37:16] Github #3723: Fingerprint crash for mols with Zero order bonds -134/208 Test #108: testFingerprints ....................... Passed 6.98 sec +129: [16:03:41] Molecule does not have explicit Hs. Consider calling AddHs() +129: [16:03:41] Molecule does not have explicit Hs. Consider calling AddHs() +129: [16:03:41] Molecule does not have explicit Hs. Consider calling AddHs() +129: [16:03:41] Molecule does not have explicit Hs. Consider calling AddHs() +129: [16:03:41] Molecule does not have explicit Hs. Consider calling AddHs() +129: [16:03:41] Molecule does not have explicit Hs. Consider calling AddHs() +129: [16:03:41] Molecule does not have explicit Hs. Consider calling AddHs() +129: [16:03:41] Molecule does not have explicit Hs. Consider calling AddHs() +129: [16:03:41] Molecule does not have explicit Hs. Consider calling AddHs() +129: [16:03:41] Molecule does not have explicit Hs. Consider calling AddHs() +141: ...........................................[16:03:44] The provided InitialSeed is not an MCS and will be ignored +141: [16:03:44] The provided InitialSeed is not an MCS and will be ignored +141: [16:03:44] The provided InitialSeed is not an MCS and will be ignored +141: .[16:03:44] The provided InitialSeed is not an MCS and will be ignored +141: [16:03:44] The provided InitialSeed is not an MCS and will be ignored +141: [16:03:44] The provided InitialSeed is not an MCS and will be ignored +141: .[16:03:44] The provided InitialSeed is not an MCS and will be ignored +141: [16:03:44] The provided InitialSeed is not an MCS and will be ignored +141: [16:03:44] The provided InitialSeed is not an MCS and will be ignored +141: .[16:03:44] The provided InitialSeed is not an MCS and will be ignored +141: [16:03:44] The provided InitialSeed is not an MCS and will be ignored +141: [16:03:44] The provided InitialSeed is not an MCS and will be ignored +141: ................. +141: ---------------------------------------------------------------------- +141: Ran 63 tests in 7.739s +141: +141: OK +143/208 Test #141: pyFMCS ................................. Passed 8.05 sec test 150 Start 150: deprotectTest 150: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/deprotectTest 150: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect 150: Test timeout computed to be: 1500 -125: [19:37:16] Molecule does not have explicit Hs. Consider calling AddHs() 150: =============================================================================== 150: All tests passed (111 assertions in 3 test cases) 150: -135/208 Test #150: deprotectTest .......................... Passed 0.09 sec +144/208 Test #150: deprotectTest .......................... Passed 0.10 sec test 151 Start 151: pyDeprotect 151: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Wrap/rough_test.py" 151: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/Wrap 151: Test timeout computed to be: 1500 -137: file testGithub4323_3.png gave hash 747920275U not the expected 2300228708U -137: [19:37:16] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. -137: file testDarkMode.1.svg gave hash 581654272U not the expected 1977391752U -137: file testMonochrome.1.svg gave hash 3944998716U not the expected 1776897420U -137: file testMonochrome.2.svg gave hash 3145122308U not the expected 399259780U -97: =>start test GETAWAY custom -97: [19:37:16] test on : 365 molecules done -136/208 Test #97: testRDFcustom .......................... Passed 8.49 sec -test 152 - Start 152: testReducedGraphs - -152: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs -152: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs -152: Test timeout computed to be: 1500 -137: file testAvalon.1.svg gave hash 22748787U not the expected 1614166818U -137: file testCDK.1.svg gave hash 4152035316U not the expected 3108685638U -137: file testGithub4519_1.svg gave hash 4122076507U not the expected 473230604U -137: file testGithub4519_2.svg gave hash 2169321355U not the expected 2515716875U -152: 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, ] -152: -152: 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, ] -152: -152: 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, ] -152: -152: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1.3, 1.3, 0.6, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] -152: -152: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1.3, 1.3, 0.6, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] -152: -152: 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, ] -152: -152: 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, ] -152: -152: 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, ] -152: -152: 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, ] -152: -137/208 Test #152: testReducedGraphs ...................... Passed 0.05 sec -test 153 - Start 153: pyReducedGraphs - -153: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" -153: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap -153: Test timeout computed to be: 1500 -137: file testGithub4519_4.svg gave hash 1879311203U not the expected 645908829U 151: ..... 151: ---------------------------------------------------------------------- -151: Ran 5 tests in 0.054s +151: Ran 5 tests in 0.058s 151: 151: OK 151: Testing tert-butyldimethylsilyl @@ -27009,623 +27861,903 @@ 151: Testing acetamide 151: Testing carbobenzyloxy 151: Testing Acetal/Ketal -137: file testBaseFontSize.1a.svg gave hash 4246301187U not the expected 3939288880U -138/208 Test #151: pyDeprotect ............................ Passed 0.30 sec +145/208 Test #151: pyDeprotect ............................ Passed 0.36 sec +test 152 + Start 152: testReducedGraphs + +152: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs +152: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs +152: Test timeout computed to be: 1500 +152: 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, ] +152: +152: 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, ] +152: +152: 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, ] +152: +152: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1.3, 1.3, 0.6, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] +152: +152: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1.3, 1.3, 0.6, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] +152: +152: 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, ] +152: +152: 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, ] +152: +152: 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, ] +152: +152: 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, ] +152: +146/208 Test #152: testReducedGraphs ...................... Passed 0.06 sec +test 153 + Start 153: pyReducedGraphs + +153: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" +153: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap +153: Test timeout computed to be: 1500 +153: ..... +153: ---------------------------------------------------------------------- +153: Ran 5 tests in 0.024s +153: +153: OK +147/208 Test #153: pyReducedGraphs ........................ Passed 0.32 sec test 154 Start 154: trajectoryTest 154: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest 154: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory 154: Test timeout computed to be: 1500 -153: ..... -153: ---------------------------------------------------------------------- -153: Ran 5 tests in 0.020s -153: -153: OK -139/208 Test #153: pyReducedGraphs ........................ Passed 0.26 sec +129: ...[16:03:45] Molecule does not have explicit Hs. Consider calling AddHs() +129: [16:03:45] Molecule does not have explicit Hs. Consider calling AddHs() +129: [16:03:45] Molecule does not have explicit Hs. Consider calling AddHs() +129: [16:03:45] Molecule does not have explicit Hs. Consider calling AddHs() +129: [16:03:45] Molecule does not have explicit Hs. Consider calling AddHs() +148/208 Test #154: trajectoryTest ......................... Passed 0.74 sec test 155 Start 155: substructLibraryTest 155: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest 155: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary 155: Test timeout computed to be: 1500 -155: [19:37:16] ------------------------------------- -155: [19:37:16] Test1 -137: file testFlexiCanvas.2a.png gave hash 3596300350U not the expected 3618977786U -137: file testFlexiCanvas.2b.png gave hash 868015450U not the expected 2780757414U -137: file testFlexiCanvas.3.svg gave hash 1188140086U not the expected 1164132085U -137: file testGithub4764.sz1.svg gave hash 2429181530U not the expected 493786705U -137: file testGithub4764.sz2.svg gave hash 1556078230U not the expected 2704253898U -137: file testGithub4764.sz3.svg gave hash 1187691699U not the expected 1328896014U -137: file testGithub4764.sz1.png gave hash 2569031563U not the expected 2320783268U -155: [19:37:16] done -137: file testGithub4764.sz2.png gave hash 3525848942U not the expected 3297570843U -155: [19:37:16] ------------------------------------- -155: [19:37:16] Test2 -140/208 Test #154: trajectoryTest ......................... Passed 0.43 sec +155: [16:03:46] ------------------------------------- +155: [16:03:46] Test1 +129: ... +129: ---------------------------------------------------------------------- +129: Ran 18 tests in 22.172s +129: +129: OK +129: Testing MolAlign Wrappers +149/208 Test #129: pyMolAlign ............................. Passed 22.50 sec test 156 Start 156: substructLibraryCatchTest 156: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest 156: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary 156: Test timeout computed to be: 1500 -137: file testGithub4764.sz3.png gave hash 2491935504U not the expected 2178018272U -137: file testDrawArc1.svg gave hash 305186657U not the expected 4039810147U -137: file testGithub_5269_1.svg gave hash 3635725957U not the expected 2368496794U -137: file testGithub_5269_2.svg gave hash 607835614U not the expected 567813292U -137: file github5383_1.png gave hash 93990453U not the expected 2963331215U -137: file github5156_2.svg gave hash 1130781980U not the expected 2606649270U -137: file github5156_3.svg gave hash 3982691065U not the expected 3284451122U -127: *********************************************************** -127: Testing O3AAlign -127: --------------------------------- -127: testMMFFO3A -127: -127: --------------------------------- -127: testMMFFO3A with pre-computed dmat and MolHistogram -127: -127: --------------------------------- -127: testMMFFO3A with constraints -127: -127: --------------------------------- -127: testMMFFO3A with variable weight constraints followed by local-only optimization -127: -127: --------------------------------- -127: testCrippenO3A -127: -127: --------------------------------- -127: testCrippenO3A with pre-computed dmat and MolHistogram -127: -127: --------------------------------- -127: testCrippenO3A with constraints -127: -127: --------------------------------- -127: testCrippenO3A with variable weight constraints followed by local-only optimization -127: -127: --------------------------------- -127: testMMFFO3A multithreading -127: -127: generating reference data -137: file acs1996_1.png gave hash 4036198339U not the expected 2674458798U -137: file acs1996_2.png gave hash 3786285444U not the expected 83755168U -137: file acs1996_4.svg gave hash 2040630632U not the expected 3372558370U -137: file acs1996_7.svg gave hash 2718384395U not the expected 763391533U -137: file acs1996_8.svg gave hash 1449819718U not the expected 939325262U -137: file acs1996_11.svg gave hash 4001805189U not the expected 2121789178U -137: [19:37:17] 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. -137: file bond_highlights_4.svg gave hash 2068128924U not the expected 4115973245U -140: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds -140: Time elapsed 0.004 seconds -140: -140: test32() -140: 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 -140: Time elapsed 0.161 seconds -140: -140: test190() -140: 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 -140: Time elapsed 0.025 seconds -140: -140: test3() -140: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds -140: Time elapsed 0.039 seconds -140: -140: testSimpleFast() -140: 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 -140: Time elapsed 0.331 seconds -140: -140: testSimple() -140: MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -140: Time elapsed 0.165 seconds -140: MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -140: Time elapsed 0.157 seconds -140: MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -140: Time elapsed 0.162 seconds -140: -140: testSegFault() -140: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -140: Time elapsed 0.013 seconds -140: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -140: Time elapsed 0.015 seconds -140: MCS MatchFusedRingsStrict: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -140: Time elapsed 0.018 seconds -140: -140: testThreshold() -140: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -140: Time elapsed 0.000 seconds -140: -140: testRing1() -140: 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 -140: Time elapsed 0.737 seconds -140: 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 -140: Time elapsed 0.367 seconds -140: MCS MatchFusedRingsStrict: [#6]1:&@[#6]:&@[#7]:&@[#6](:&@[#6]:&@[#6]:&@1)-&!@[#6](=&!@[#8])-&!@[#8]-&!@[#6](-&!@[#6])-&!@[#6] 12 atoms, 12 bonds -140: Time elapsed 0.339 seconds -140: -140: testAtomCompareIsotopes() -140: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds -140: Time elapsed 0.005 seconds -140: -140: testAtomCompareAnyAtom() -140: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds -140: Time elapsed 0.000 seconds -140: -140: testAtomCompareAnyAtom() -140: MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds -140: Time elapsed 0.000 seconds -140: -140: testAtomCompareAnyAtom() -140: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds -140: Time elapsed 0.000 seconds -140: -140: testAtomCompareAnyAtom() -140: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds -140: Time elapsed 0.000 seconds -140: -140: testJnk1LigandsDistance() -140: 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 -140: Time elapsed 0.012 seconds -140: 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 -137: file bond_highlights_8.svg gave hash 1796268304U not the expected 3826056528U -137: =============================================================================== -137: All tests passed (379 assertions in 67 test cases) -137: -141/208 Test #137: moldraw2DTestCatch ..................... Passed 4.25 sec +155: [16:03:46] done +156: =============================================================================== +156: All tests passed (111 assertions in 4 test cases) +156: +155: [16:03:46] ------------------------------------- +155: [16:03:46] Test2 +150/208 Test #156: substructLibraryCatchTest .............. Passed 0.17 sec test 157 Start 157: pySubstructLibrary 157: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" 157: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap 157: Test timeout computed to be: 1500 -156: =============================================================================== -156: All tests passed (111 assertions in 4 test cases) -156: -142/208 Test #156: substructLibraryCatchTest .............. Passed 0.18 sec +155: [16:03:46] done +155: [16:03:46] ------------------------------------- +155: [16:03:46] Test3 (stereo options) +155: [16:03:46] Done (stereo options) +155: [16:03:46] ------------------------------------- +155: [16:03:46] Test4 (trusted smiles) +155: [16:03:46] Done (trusted smiles) +155: [16:03:46] ------------------------------------- +155: [16:03:46] Testing C++ docs +155: [16:03:46] Done (C++ doc tests) +155: [16:03:46] ------------------------------------- +155: [16:03:46] Testing C++ ring query: PatternHolder +155: [16:03:46] Done (C++ ring query tests) +155: [16:03:46] ------------------------------------- +155: [16:03:46] Testing C++ ring query: TautomerPatternHolder +155: [16:03:46] Done (C++ ring query tests) +155: [16:03:46] ------------------------------------- +155: [16:03:46] Add Patterns +155: [16:03:49] ------------------------------------- +155: [16:03:49] testing PatternHolder +155: [16:03:49] ------------------------------------- +155: [16:03:49] testing TautomerPatternHolder +155: [16:03:49] ------------------------------------- +155: [16:03:49] testSegFaultInHolder +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: ' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [16:03:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [16:03:49] ------------------------------------- +155: [16:03:49] Results do not depend on numThreads +149: VS001: PASSED +149: VS002: PASSED +149: VS003: PASSED +149: VS004: PASSED +149: VS005: PASSED +149: VS006: PASSED +149: VS007: PASSED +149: VS008: PASSED +149: VS009: PASSED +149: VS010: PASSED +149: VS011: PASSED +149: VS012: PASSED +149: VS013: PASSED +149: VS014: PASSED +149: VS015: PASSED +149: VS016: PASSED +149: VS017: PASSED +149: VS018: PASSED +149: VS019: PASSED +149: VS020: PASSED +149: VS021: PASSED +149: VS022: PASSED +149: VS023: PASSED +149: VS024: PASSED +149: VS025: PASSED +149: VS026: PASSED +149: VS027: PASSED +149: VS028: PASSED +149: VS029: PASSED +149: VS030: PASSED +149: VS031: PASSED +149: VS032: PASSED +149: VS033: PASSED +149: VS034: PASSED +149: VS035: PASSED +149: VS036: PASSED +149: VS037: PASSED +149: VS038: PASSED +149: VS039: PASSED +149: VS040: PASSED +149: VS041: PASSED +149: VS042: PASSED +149: VS043: PASSED +149: VS044: PASSED +149: VS045: PASSED +149: VS046: PASSED +149: VS047: PASSED +149: VS048: PASSED +149: VS049: PASSED +149: VS050: PASSED +149: VS051: PASSED +149: VS052: PASSED +149: VS053: PASSED +149: VS054: PASSED +149: VS055: PASSED +149: VS056: PASSED +149: VS057: PASSED +149: VS058: PASSED +149: VS059: PASSED +149: VS060: PASSED +149: VS061: PASSED +149: VS062: PASSED +149: VS063: PASSED +149: VS064: PASSED +149: VS065: PASSED +149: VS066: PASSED +149: VS067: PASSED +149: VS068: PASSED +149: VS069: PASSED +149: VS070: PASSED +149: VS071: PASSED +149: VS072: PASSED +149: VS073: PASSED +149: VS074: PASSED +149: VS075: PASSED +149: VS076: PASSED +149: VS077: PASSED +149: VS078: PASSED +149: VS079: PASSED +149: VS080: PASSED +149: VS081: PASSED +149: VS082: PASSED +149: VS083: PASSED +149: VS084: PASSED +149: VS085: PASSED +149: VS086: PASSED +149: VS087: PASSED +149: VS088: PASSED +149: VS089: PASSED +149: VS090: PASSED +149: VS091: PASSED +149: VS092: PASSED +149: VS093: PASSED +149: VS094: PASSED +149: VS095: PASSED +149: VS096: PASSED +149: VS097: PASSED +149: VS098: PASSED +149: VS099: PASSED +149: VS100: PASSED +149: VS101: PASSED +149: VS102: PASSED +149: VS103: PASSED +149: VS104: PASSED +149: VS105: PASSED +149: VS106: PASSED +149: VS107: PASSED +149: VS108: PASSED +149: VS109: PASSED +149: VS110: PASSED +149: VS111: PASSED +149: VS112: PASSED +149: VS113: PASSED +149: VS114: PASSED +149: VS115: PASSED +149: VS116: PASSED +149: VS117: PASSED +149: VS118: PASSED +149: VS119: PASSED +149: VS120: PASSED +149: VS121: PASSED +149: VS122: PASSED +149: VS123: PASSED +149: VS124: PASSED +149: VS125: PASSED +149: VS126: PASSED +149: VS127: PASSED +149: VS128: PASSED +149: VS129: PASSED +149: VS130: PASSED +149: VS131: PASSED +149: VS132: PASSED +149: VS133: PASSED +149: VS134: PASSED +149: VS135: PASSED +149: VS136: PASSED +149: VS137: PASSED +149: VS138: PASSED +149: VS139: PASSED +149: VS140: PASSED +149: VS141: PASSED +149: VS142: PASSED +149: VS143: PASSED +149: VS144: PASSED +149: VS145: PASSED +149: VS146: PASSED +149: VS147: PASSED +149: VS148: PASSED +149: VS149: PASSED +149: VS150: PASSED +149: VS151: PASSED +149: VS152: PASSED +149: VS153: PASSED +149: VS154: PASSED +149: VS155: PASSED +149: VS156: PASSED +149: VS157: PASSED +149: VS158: PASSED +149: VS159: PASSED +149: VS160: PASSED +149: VS161: PASSED +149: VS162: PASSED +149: VS163: PASSED +149: VS164: PASSED +149: VS165: PASSED +149: VS166: PASSED +149: VS167: PASSED +149: VS168: PASSED +149: VS169: PASSED +149: VS170: PASSED +149: VS171: PASSED +149: VS172: PASSED +149: VS173: PASSED +149: VS174: PASSED +149: VS175: PASSED +149: VS176: PASSED +149: VS177: PASSED +149: VS178: PASSED +149: VS179: PASSED +149: VS180: PASSED +149: VS181: PASSED +149: VS182: PASSED +149: VS183: PASSED +149: VS184: PASSED +149: VS185: PASSED +149: VS186: PASSED +149: VS187: PASSED +149: VS188: PASSED +149: VS189: PASSED +149: VS190: PASSED +149: VS191: PASSED +149: VS192: PASSED +149: VS193: PASSED +149: VS194: PASSED +149: VS195: PASSED +149: VS196: PASSED +149: VS197: PASSED +149: VS198: PASSED +149: VS199: PASSED +149: VS200: PASSED +149: VS201: PASSED +149: VS202: PASSED +149: VS203: PASSED +149: VS204: PASSED +149: VS205: PASSED +149: VS206: PASSED +149: VS207: PASSED +149: VS208: PASSED +149: VS209: PASSED +149: VS210: PASSED +149: VS211: PASSED +149: VS212: PASSED +149: VS213: PASSED +149: VS214: PASSED +149: VS215: PASSED +149: VS216: PASSED +149: VS217: PASSED +149: VS218: PASSED +149: VS219: PASSED +149: VS220: PASSED +149: VS221: PASSED +149: VS222: PASSED +149: VS223: PASSED +149: VS224: PASSED +149: VS225: PASSED +149: VS226: PASSED +149: VS227: PASSED +149: VS228: PASSED +149: VS229: PASSED +149: VS230: PASSED +149: VS231: PASSED +149: VS232: PASSED +149: VS233: PASSED +149: VS234: PASSED +149: VS235: PASSED +149: VS236: PASSED +149: VS237: PASSED +149: VS238: PASSED +149: VS239: PASSED +149: VS240: PASSED +149: VS241: PASSED +149: VS242: PASSED +149: VS243: PASSED +149: VS244: PASSED +149: VS245: PASSED +149: VS246: PASSED +149: VS247: PASSED +149: VS248: PASSED +149: VS249: PASSED +149: VS250: PASSED +149: VS251: PASSED +149: VS252: PASSED +149: VS253: PASSED +149: VS254: PASSED +149: VS255: PASSED +149: VS256: PASSED +149: VS257: PASSED +149: VS258: PASSED +149: VS259: PASSED +149: VS260: PASSED +149: VS261: PASSED +149: VS262: PASSED +149: VS263: PASSED +149: VS264: PASSED +149: VS265: PASSED +149: VS266: PASSED +149: VS267: PASSED +149: VS268: PASSED +149: VS269: PASSED +149: VS270: PASSED +149: VS271: PASSED +149: VS272: PASSED +149: VS273: PASSED +149: VS274: PASSED +149: VS275: PASSED +149: VS276: PASSED +149: VS277: PASSED +149: VS278: PASSED +149: VS279: PASSED +149: VS280: PASSED +149: VS281: PASSED +149: VS282: PASSED +149: VS283: PASSED +149: VS284: PASSED +149: VS285: PASSED +149: VS286: PASSED +149: VS287: PASSED +149: VS288: PASSED +149: VS289: PASSED +149: VS290: PASSED +149: VS291: PASSED +149: VS292: PASSED +149: VS293: PASSED +149: VS294: PASSED +149: VS295: PASSED +149: VS296: PASSED +149: VS297: PASSED +149: VS298: PASSED +149: VS299: PASSED +149: VS300: PASSED +149: Check finished: 0 molecules failed. +149: Failed: +151/208 Test #149: pyCIPLabelsValidation .................. Passed 12.75 sec test 158 Start 158: testRGroupDecomp 158: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp 158: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition 158: Test timeout computed to be: 1500 -125: .[19:37:17] Molecule does not have explicit Hs. Consider calling AddHs() -155: [19:37:17] done -155: [19:37:17] ------------------------------------- -155: [19:37:17] Test3 (stereo options) -146: ......... -146: ---------------------------------------------------------------------- -146: Ran 9 tests in 1.589s -146: -146: OK -155: [19:37:17] Done (stereo options) -155: [19:37:17] ------------------------------------- -155: [19:37:17] Test4 (trusted smiles) -143/208 Test #146: pyMMPA ................................. Passed 1.87 sec +158: [16:03:54] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters +158: [16:03:54] WARNING: not removing hydrogen atom with dummy atom neighbors +155: [16:03:54] ------------------------------------- +155: [16:03:54] Results do not depend on numThreads (all same) +155: [16:03:54] ------------------------------------- +155: [16:03:54] testTautomerQueries +155: [16:03:55] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... +155: [16:03:55] ------------------------------------- +155: [16:03:55] github3881 recursive smarts with rings +152/208 Test #155: substructLibraryTest ................... Passed 8.98 sec test 159 Start 159: testRGroupDecompInternals 159: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals 159: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition 159: Test timeout computed to be: 1500 -140: Time elapsed 0.002 seconds -140: -140: test18() -140: 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 -140: 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 -140: Time elapsed 0.010 seconds -140: -140: test504() -140: 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 -140: 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 -140: Time elapsed 0.128 seconds -140: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds -140: Time elapsed 0.002 seconds -140: 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 -140: Time elapsed 0.038 seconds -140: Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds -140: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0012 seconds. bond[0]=6 -140: STATISTICS: -140: Total Growing Steps = 1, MCS found on 1 step, for 0.0012 seconds -140: Initial Seeds = 1, Mismatched 0 -140: Inspected Seeds = 2 -140: Rejected by BestSize = 0 -140: SingleBondExcluded = 0 -140: MatchCheck Seeds = 2 -140: MatchCalls = 2 -140: MatchFound = 1 -140: fastMatchCalls = 1 -140: fastMatchFound = 0 -140: slowMatchCalls = 2 -140: slowMatchFound = 1 -140: DupCacheFound = 0 0 matched, 0 mismatched -140: HashCache size = 1 keys -140: HashCache size = 1 entries -140: FindHashInCache = 2 -140: HashFoundInCache= 0 -140: ExactMatchCalls = 0 -140: ExactMatchFound = 0 -140: Time elapsed 0.002 seconds -140: query=OCCl SubstructMatch(useChirality=false) res =1 size=3 -140: query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 -140: test target = O[C@H](F)CCl query = C(F)C useChirality = 0 -140: res sub = 1 size=3 -140: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds -140: test target = O[C@H](F)CCl query = C(F)C useChirality = 1 -140: res sub = 1 size=3 -140: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds -140: test target = CC[C@H](F)Cl query = CCC useChirality = 0 -140: res sub = 1 size=3 -140: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -140: test target = CC[C@H](F)Cl query = CCC useChirality = 1 -140: res sub = 1 size=3 -140: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -140: test target = CCC(F)Cl query = CC useChirality = 0 -140: res sub = 1 size=2 -140: MCS: [#6]-[#6] 2 atoms, 1 bonds -140: test target = CCC(F)Cl query = CC useChirality = 1 -140: res sub = 1 size=2 -140: MCS: [#6]-[#6] 2 atoms, 1 bonds -140: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 0 -140: res sub = 1 size=4 -140: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -140: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 1 -140: res sub = 1 size=4 -140: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -140: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 0 -140: res sub = 1 size=4 -140: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -140: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 1 -140: res sub = 1 size=4 -140: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -140: test target = O[C@H](F)CCl query = CC(F)C useChirality = 0 -140: res sub = 0 size=0 -140: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds -140: test target = O[C@H](F)CCl query = CC(F)C useChirality = 1 -140: res sub = 0 size=0 -140: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds -140: test target = O[C@H](F)CCl query = OC(F)C useChirality = 0 -140: res sub = 1 size=4 -140: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -140: test target = O[C@H](F)CCl query = OC(F)C useChirality = 1 -140: res sub = 1 size=4 -140: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -140: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 0 -140: res sub = 1 size=4 -140: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -140: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 1 -140: res sub = 1 size=4 -140: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -140: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 0 -140: res sub = 1 size=4 -140: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -140: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 1 -140: res sub = 0 size=0 -140: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -140: test target = OC(F)CCl query = OC(F)C useChirality = 0 -140: res sub = 1 size=4 -140: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -140: test target = OC(F)CCl query = OC(F)C useChirality = 1 -140: res sub = 1 size=4 -140: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -140: test target = OC(F)CCl query = O[C@H](F)C useChirality = 0 -140: res sub = 1 size=4 -140: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -140: test target = OC(F)CCl query = O[C@H](F)C useChirality = 1 -140: res sub = 0 size=0 -140: MCS: [#9] 1 atoms, 0 bonds -140: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 0 -140: res sub = 1 size=4 -140: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -140: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 1 -140: res sub = 0 size=0 -140: MCS: [#9] 1 atoms, 0 bonds -140: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 0 -140: res sub = 1 size=3 -140: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -140: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 1 -140: res sub = 1 size=3 -140: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -140: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 0 -140: res sub = 1 size=3 -140: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -140: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 1 -140: res sub = 1 size=3 -140: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -140: -140: 0. <<<<<<<<< actual MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds >>>>>>> -140: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 0 -140: res sub = 1 size=3 -140: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -140: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 1 -140: res sub = 1 size=3 -140: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -140: done -159: [19:37:17] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [19:37:17] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [19:37:17] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [19:37:17] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [19:37:17] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [19:37:17] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [19:37:17] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [19:37:17] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [19:37:17] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [19:37:17] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [19:37:17] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [19:37:17] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [19:37:17] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [19:37:17] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [19:37:17] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [19:37:17] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [19:37:17] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [19:37:17] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [19:37:17] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [19:37:17] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [19:37:17] WARNING: not removing hydrogen atom with dummy atom neighbors -144/208 Test #159: testRGroupDecompInternals .............. Passed 0.04 sec +159: [16:03:55] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [16:03:55] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [16:03:55] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [16:03:55] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [16:03:55] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [16:03:55] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [16:03:55] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [16:03:55] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [16:03:55] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [16:03:55] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [16:03:55] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [16:03:55] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [16:03:55] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [16:03:55] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [16:03:55] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [16:03:55] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [16:03:55] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [16:03:55] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [16:03:55] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [16:03:55] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [16:03:55] WARNING: not removing hydrogen atom with dummy atom neighbors +153/208 Test #159: testRGroupDecompInternals .............. Passed 0.04 sec test 160 Start 160: rgroupCatchTests 160: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests 160: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition 160: Test timeout computed to be: 1500 -140: MCS: [#6]1-&@[#6](-&!@[#6])-&@[#6]-&@[#6]-&@[#6]-&@[#6]-&@1 7 atoms, 7 bonds -140: -140: MCS: [#6]-&!@[#6] 2 atoms, 1 bonds -140: -155: [19:37:17] Done (trusted smiles) -155: [19:37:17] ------------------------------------- -155: [19:37:17] Testing C++ docs -155: [19:37:17] Done (C++ doc tests) -155: [19:37:17] ------------------------------------- -155: [19:37:17] Testing C++ ring query: PatternHolder -155: [19:37:17] Done (C++ ring query tests) -155: [19:37:17] ------------------------------------- -155: [19:37:17] Testing C++ ring query: TautomerPatternHolder -155: [19:37:17] Done (C++ ring query tests) -155: [19:37:17] ------------------------------------- -155: [19:37:17] Add Patterns 160: =============================================================================== 160: All tests passed (142 assertions in 10 test cases) 160: -145/208 Test #160: rgroupCatchTests ....................... Passed 0.18 sec +154/208 Test #160: rgroupCatchTests ....................... Passed 0.20 sec test 161 Start 161: pyRGroupDecomposition 161: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py" 161: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap 161: Test timeout computed to be: 1500 -158: [19:37:17] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters -158: [19:37:17] WARNING: not removing hydrogen atom with dummy atom neighbors -140: [19:37:17] -140: -140: **** -140: Test Assert -140: Expression Failed: -140: Violation occurred on line 2326 in file ./Code/GraphMol/FMCS/testFMCS_Unit.cpp -140: Failed Expression: res.NumAtoms == 17 -140: **** -140: -140: terminate called after throwing an instance of 'Invar::Invariant' -140: what(): Expression Failed: -146/208 Test #140: testFMCS ...............................Subprocess aborted***Exception: 3.23 sec -MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds -Time elapsed 0.004 seconds - - test32() -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 -Time elapsed 0.161 seconds - - test190() -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 -Time elapsed 0.025 seconds - - test3() -MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds -Time elapsed 0.039 seconds - -testSimpleFast() -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 -Time elapsed 0.331 seconds - -testSimple() -MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -Time elapsed 0.165 seconds -MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -Time elapsed 0.157 seconds -MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -Time elapsed 0.162 seconds - -testSegFault() -MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -Time elapsed 0.013 seconds -MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -Time elapsed 0.015 seconds -MCS MatchFusedRingsStrict: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -Time elapsed 0.018 seconds - -testThreshold() -MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -Time elapsed 0.000 seconds - -testRing1() -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 -Time elapsed 0.737 seconds -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 -Time elapsed 0.367 seconds -MCS MatchFusedRingsStrict: [#6]1:&@[#6]:&@[#7]:&@[#6](:&@[#6]:&@[#6]:&@1)-&!@[#6](=&!@[#8])-&!@[#8]-&!@[#6](-&!@[#6])-&!@[#6] 12 atoms, 12 bonds -Time elapsed 0.339 seconds - -testAtomCompareIsotopes() -MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds -Time elapsed 0.005 seconds - -testAtomCompareAnyAtom() -MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds -Time elapsed 0.000 seconds - -testAtomCompareAnyAtom() -MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds -Time elapsed 0.000 seconds - -testAtomCompareAnyAtom() -MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds -Time elapsed 0.000 seconds - -testAtomCompareAnyAtom() -MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds -Time elapsed 0.000 seconds - -testJnk1LigandsDistance() -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 -Time elapsed 0.012 seconds -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 -Time elapsed 0.002 seconds - -test18() -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 -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 -Time elapsed 0.010 seconds - -test504() -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 -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 -Time elapsed 0.128 seconds -MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds -Time elapsed 0.002 seconds -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 -Time elapsed 0.038 seconds -Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds -1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0012 seconds. bond[0]=6 -STATISTICS: -Total Growing Steps = 1, MCS found on 1 step, for 0.0012 seconds -Initial Seeds = 1, Mismatched 0 -Inspected Seeds = 2 -Rejected by BestSize = 0 -SingleBondExcluded = 0 -MatchCheck Seeds = 2 - MatchCalls = 2 - MatchFound = 1 - fastMatchCalls = 1 - fastMatchFound = 0 - slowMatchCalls = 2 - slowMatchFound = 1 - DupCacheFound = 0 0 matched, 0 mismatched -HashCache size = 1 keys -HashCache size = 1 entries -FindHashInCache = 2 -HashFoundInCache= 0 -ExactMatchCalls = 0 -ExactMatchFound = 0 -Time elapsed 0.002 seconds -query=OCCl SubstructMatch(useChirality=false) res =1 size=3 -query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 -test target = O[C@H](F)CCl query = C(F)C useChirality = 0 -res sub = 1 size=3 -MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds -test target = O[C@H](F)CCl query = C(F)C useChirality = 1 -res sub = 1 size=3 -MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds -test target = CC[C@H](F)Cl query = CCC useChirality = 0 -res sub = 1 size=3 -MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -test target = CC[C@H](F)Cl query = CCC useChirality = 1 -res sub = 1 size=3 -MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -test target = CCC(F)Cl query = CC useChirality = 0 -res sub = 1 size=2 -MCS: [#6]-[#6] 2 atoms, 1 bonds -test target = CCC(F)Cl query = CC useChirality = 1 -res sub = 1 size=2 -MCS: [#6]-[#6] 2 atoms, 1 bonds -test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 0 -res sub = 1 size=4 -MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 1 -res sub = 1 size=4 -MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 0 -res sub = 1 size=4 -MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 1 -res sub = 1 size=4 -MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -test target = O[C@H](F)CCl query = CC(F)C useChirality = 0 -res sub = 0 size=0 -MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds -test target = O[C@H](F)CCl query = CC(F)C useChirality = 1 -res sub = 0 size=0 -MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds -test target = O[C@H](F)CCl query = OC(F)C useChirality = 0 -res sub = 1 size=4 -MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -test target = O[C@H](F)CCl query = OC(F)C useChirality = 1 -res sub = 1 size=4 -MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 0 -res sub = 1 size=4 -MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 1 -res sub = 1 size=4 -MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 0 -res sub = 1 size=4 -MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 1 -res sub = 0 size=0 -MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -test target = OC(F)CCl query = OC(F)C useChirality = 0 -res sub = 1 size=4 -MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -test target = OC(F)CCl query = OC(F)C useChirality = 1 -res sub = 1 size=4 -MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -test target = OC(F)CCl query = O[C@H](F)C useChirality = 0 -res sub = 1 size=4 -MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -test target = OC(F)CCl query = O[C@H](F)C useChirality = 1 -res sub = 0 size=0 -MCS: [#9] 1 atoms, 0 bonds -test target = OC(F)CCl query = O[C@@H](F)C useChirality = 0 -res sub = 1 size=4 -MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -test target = OC(F)CCl query = O[C@@H](F)C useChirality = 1 -res sub = 0 size=0 -MCS: [#9] 1 atoms, 0 bonds -test target = O[C@H](F)CCl query = O[C@H]C useChirality = 0 -res sub = 1 size=3 -MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -test target = O[C@H](F)CCl query = O[C@H]C useChirality = 1 -res sub = 1 size=3 -MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 0 -res sub = 1 size=3 -MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 1 -res sub = 1 size=3 -MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds - -0. <<<<<<<<< actual MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds >>>>>>> -test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 0 -res sub = 1 size=3 -MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 1 -res sub = 1 size=3 -MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds - done -MCS: [#6]1-&@[#6](-&!@[#6])-&@[#6]-&@[#6]-&@[#6]-&@[#6]-&@1 7 atoms, 7 bonds - -MCS: [#6]-&!@[#6] 2 atoms, 1 bonds - -[19:37:17] - -**** -Test Assert -Expression Failed: -Violation occurred on line 2326 in file ./Code/GraphMol/FMCS/testFMCS_Unit.cpp -Failed Expression: res.NumAtoms == 17 -**** - -terminate called after throwing an instance of 'Invar::Invariant' - what(): Expression Failed: - +157: ......[16:03:55] +157: +157: **** +157: Pre-condition Violation +157: RingInfo not initialized +157: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp +157: Failed Expression: df_init +157: **** +157: +157: [16:03:55] +157: +157: **** +157: Pre-condition Violation +157: RingInfo not initialized +157: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp +157: Failed Expression: df_init +157: **** +157: +161: ............... +161: ---------------------------------------------------------------------- +161: Ran 15 tests in 1.788s +161: +161: OK +155/208 Test #161: pyRGroupDecomposition .................. Passed 2.08 sec test 162 Start 162: molInterchangeTest1 @@ -27640,114 +28772,116 @@ 162: {"commonchem":{"version":10},"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":"2022.09.3","cipRanks":[0,0]}]}]} 162: {"commonchem":{"version":10},"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":"2022.09.3","cipRanks":[0,1]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2022.09.3","values":[0.5,-0.5]}]}]} 162: {"commonchem":{"version":10},"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":"2022.09.3","cipRanks":[1,0,2,4,3,5],"cipCodes":[[4,"S"]],"atomRings":[[0,1,2,3,4]]}]}]} -147/208 Test #162: molInterchangeTest1 .................... Passed 0.05 sec +156/208 Test #162: molInterchangeTest1 .................... Passed 0.05 sec test 163 Start 163: molInterchangeCatchTest 163: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest 163: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange 163: Test timeout computed to be: 1500 -163: [19:37:17] unrecognized bond type set to zero while writing -163: [19:37:17] unrecognized bond type set to zero while writing +163: [16:03:57] unrecognized bond type set to zero while writing +163: [16:03:57] unrecognized bond type set to zero while writing 163: =============================================================================== 163: All tests passed (14 assertions in 1 test case) 163: -148/208 Test #163: molInterchangeCatchTest ................ Passed 0.04 sec +157/208 Test #163: molInterchangeCatchTest ................ Passed 0.04 sec test 164 Start 164: pyMolInterchange 164: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" 164: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap 164: Test timeout computed to be: 1500 -123: validating reference data 164: . 164: ---------------------------------------------------------------------- -164: Ran 1 test in 0.015s +164: Ran 1 test in 0.033s 164: 164: OK -149/208 Test #164: pyMolInterchange ....................... Passed 0.27 sec +158/208 Test #164: pyMolInterchange ....................... Passed 0.44 sec test 165 Start 165: testSLNParse 165: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse/testSLNParse 165: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse 165: Test timeout computed to be: 1500 -165: [19:37:17] SLN Parse Error: syntax error while parsing: CH4[I=13] -165: [19:37:17] Failed parsing SLN 'CH4[I=13]' -165: [19:37:17] SLN Parser error: Atom ID 1 appears *after* its ring closure. -165: [19:37:17] SLN Parser error: Ring closure 1 does not have a corresponding opener. -165: [19:37:17] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) -165: [19:37:17] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' -165: [19:37:17] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) -165: [19:37:17] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' -165: [19:37:17] SLN Parse Error: syntax error while parsing: CH4 fff -165: [19:37:17] Failed parsing SLN 'CH4 fff' -165: [19:37:17] SLN Parse Error: syntax error while parsing: C[charge=+1] foo -165: [19:37:17] Failed parsing SLN 'C[charge=+1] foo' -165: [19:37:17] Query property 'is' ignored on non-query atom -165: [19:37:17] Query property 'is' ignored on non-query atom -150/208 Test #165: testSLNParse ........................... Passed 0.05 sec +165: [16:03:57] SLN Parse Error: syntax error while parsing: CH4[I=13] +165: [16:03:57] Failed parsing SLN 'CH4[I=13]' +165: [16:03:57] SLN Parser error: Atom ID 1 appears *after* its ring closure. +165: [16:03:57] SLN Parser error: Ring closure 1 does not have a corresponding opener. +165: [16:03:57] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) +165: [16:03:57] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' +165: [16:03:57] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) +165: [16:03:57] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' +165: [16:03:57] SLN Parse Error: syntax error while parsing: CH4 fff +165: [16:03:57] Failed parsing SLN 'CH4 fff' +165: [16:03:57] SLN Parse Error: syntax error while parsing: C[charge=+1] foo +165: [16:03:57] Failed parsing SLN 'C[charge=+1] foo' +165: [16:03:57] Query property 'is' ignored on non-query atom +165: [16:03:57] Query property 'is' ignored on non-query atom +159/208 Test #165: testSLNParse ........................... Passed 0.06 sec test 166 Start 166: pySLNParse 166: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/Wrap/testSLN.py" 166: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap 166: Test timeout computed to be: 1500 +127: --------------------------------- +127: test O3A multithreading bug +127: +127: --------------------------------- +127: testCrippenO3A multithreading +127: +127: generating reference data 166: /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/Wrap/testSLN.py:50: DeprecationWarning: Please use assertTrue instead. 166: self.failUnless(m1) 166: .. 166: ---------------------------------------------------------------------- -166: Ran 2 tests in 0.014s +166: Ran 2 tests in 0.016s 166: 166: OK -151/208 Test #166: pySLNParse ............................. Passed 0.26 sec +160/208 Test #166: pySLNParse ............................. Passed 0.29 sec test 167 Start 167: pyGraphMolWrap 167: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rough_test.py" 167: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap 167: Test timeout computed to be: 1500 -127: processing -127: launch :0 -127: launch :1 -127: launch :2 -127: launch :3 -167: ..............[19:37:18] SMARTS Parse Error: syntax error while parsing: fiib -167: [19:37:18] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' -167: ....[19:37:18] ERROR: Problems encountered parsing data fields -167: [19:37:18] ERROR: moving to the beginning of the next molecule -167: [19:37:18] ERROR: Problems encountered parsing data fields -167: [19:37:18] ERROR: moving to the beginning of the next molecule -167: [19:37:18] Spurious data before the first property will be ignored -167: [19:37:18] Property will be truncated after the first blank line -167: [19:37:18] Property will be truncated after the first blank line -167: [19:37:18] Property will be truncated after the first blank line -167: [19:37:18] ERROR: Problems encountered parsing data fields -167: [19:37:18] ERROR: moving to the beginning of the next molecule -167: [19:37:18] ERROR: Problems encountered parsing data fields -167: [19:37:18] ERROR: moving to the beginning of the next molecule -167: [19:37:18] Spurious data before the first property will be ignored -167: [19:37:18] Property will be truncated after the first blank line -167: [19:37:18] Property will be truncated after the first blank line -167: [19:37:18] Property will be truncated after the first blank line -167: [19:37:18] ERROR: Problems encountered parsing data fields -167: [19:37:18] ERROR: moving to the beginning of the next molecule -167: [19:37:18] Property will be truncated after the first blank line -167: [19:37:18] ERROR: Problems encountered parsing data fields -167: [19:37:18] ERROR: moving to the beginning of the next molecule -167: [19:37:18] Property will be truncated after the first blank line -167: .[19:37:18] SMILES Parse Error: syntax error while parsing: fail -167: [19:37:18] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -167: [19:37:18] ERROR: Smiles parse error on line 2 -167: [19:37:18] ERROR: Cannot create molecule from : 'fail' +158: iterative +167: ..............[16:03:58] SMARTS Parse Error: syntax error while parsing: fiib +167: [16:03:58] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' +167: ....[16:03:58] ERROR: Problems encountered parsing data fields +167: [16:03:58] ERROR: moving to the beginning of the next molecule +167: [16:03:58] ERROR: Problems encountered parsing data fields +167: [16:03:58] ERROR: moving to the beginning of the next molecule +167: [16:03:58] Spurious data before the first property will be ignored +167: [16:03:58] Property will be truncated after the first blank line +167: [16:03:58] Property will be truncated after the first blank line +167: [16:03:58] Property will be truncated after the first blank line +167: [16:03:58] ERROR: Problems encountered parsing data fields +167: [16:03:58] ERROR: moving to the beginning of the next molecule +167: [16:03:58] ERROR: Problems encountered parsing data fields +167: [16:03:58] ERROR: moving to the beginning of the next molecule +167: [16:03:58] Spurious data before the first property will be ignored +167: [16:03:58] Property will be truncated after the first blank line +167: [16:03:58] Property will be truncated after the first blank line +167: [16:03:58] Property will be truncated after the first blank line +167: [16:03:58] ERROR: Problems encountered parsing data fields +167: [16:03:58] ERROR: moving to the beginning of the next molecule +167: [16:03:58] Property will be truncated after the first blank line +167: [16:03:58] ERROR: Problems encountered parsing data fields +167: [16:03:58] ERROR: moving to the beginning of the next molecule +167: [16:03:58] Property will be truncated after the first blank line +167: .[16:03:58] SMILES Parse Error: syntax error while parsing: fail +167: [16:03:58] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +167: [16:03:58] ERROR: Smiles parse error on line 2 +167: [16:03:58] ERROR: Cannot create molecule from : 'fail' 167: >>> This may result in an infinite loop. It should finish almost instantly 167: <<< OK, it finished. -167: ............[19:37:18] Explicit valence for atom # 1 C, 5, is greater than permitted +167: ............[16:03:58] Explicit valence for atom # 1 C, 5, is greater than permitted 167: ........../build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rough_test.py:2161: DeprecationWarning: Please use assertEqual instead. 167: self.assertEquals(ri.NumRings(), 2) -167: ..[19:37:18] non-ring atom 0 marked aromatic -167: [19:37:18] non-ring atom 0 marked aromatic -167: [19:37:18] +167: ..[16:03:58] non-ring atom 0 marked aromatic +167: [16:03:58] non-ring atom 0 marked aromatic +167: [16:03:58] 167: 167: **** 167: Range Error @@ -27756,9 +28890,9 @@ 167: Failed Expression: 12 < 6 167: **** 167: -167: [19:37:18] non-ring atom 0 marked aromatic -167: [19:37:18] non-ring atom 0 marked aromatic -167: [19:37:18] +167: [16:03:58] non-ring atom 0 marked aromatic +167: [16:03:58] non-ring atom 0 marked aromatic +167: [16:03:58] 167: 167: **** 167: Range Error @@ -27767,16 +28901,28 @@ 167: Failed Expression: 12 < 6 167: **** 167: -167: ...............[19:37:18] 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. -167: [19:37:18] 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. -167: ..............[19:37:18] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -167: [19:37:18] Explicit valence for atom # 1 C, 5, is greater than permitted -161: ............... -161: ---------------------------------------------------------------------- -161: Ran 15 tests in 1.596s -161: -161: OK -152/208 Test #161: pyRGroupDecomposition .................. Passed 1.87 sec +167: ...............[16:03:58] 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. +167: [16:03:58] 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. +167: ..............[16:03:58] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +167: [16:03:58] Explicit valence for atom # 1 C, 5, is greater than permitted +127: processing +127: launch :0 +127: launch :1 +127: launch :2 +127: launch :3 +158: bulk +158: bulk, no symmetry +157: ............ +157: ---------------------------------------------------------------------- +157: Ran 18 tests in 16.301s +157: +157: OK +157: Testing atom rings +157: testing bond rings +157: searching atom rings +157: searching bond rings +157: done +161/208 Test #157: pySubstructLibrary ..................... Passed 16.64 sec test 168 Start 168: pyTestConformerWrap @@ -27785,25 +28931,18 @@ 168: Test timeout computed to be: 1500 168: ...... 168: ---------------------------------------------------------------------- -168: Ran 6 tests in 0.020s +168: Ran 6 tests in 0.018s 168: 168: OK -153/208 Test #168: pyTestConformerWrap .................... Passed 0.27 sec +162/208 Test #168: pyTestConformerWrap .................... Passed 0.27 sec test 169 Start 169: pyTestTrajectory 169: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/testTrajectory.py" 169: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap 169: Test timeout computed to be: 1500 -141: ...........................................[19:37:19] The provided InitialSeed is not an MCS and will be ignored -141: [19:37:19] The provided InitialSeed is not an MCS and will be ignored -141: [19:37:19] The provided InitialSeed is not an MCS and will be ignored -141: .[19:37:19] The provided InitialSeed is not an MCS and will be ignored -141: [19:37:19] The provided InitialSeed is not an MCS and will be ignored -141: [19:37:19] The provided InitialSeed is not an MCS and will be ignored -141: .[19:37:19] The provided InitialSeed is not an MCS and will be ignored -141: [19:37:19] The provided InitialSeed is not an MCS and will be ignored -169: [19:37:19] +158: [16:04:03] Relabelling existing label +169: [16:04:03] 169: 169: **** 169: Pre-condition Violation @@ -27812,7 +28951,7 @@ 169: Failed Expression: from < static_cast(size()) 169: **** 169: -169: .[19:37:19] +169: .[16:04:03] 169: 169: **** 169: Pre-condition Violation @@ -27821,54 +28960,18 @@ 169: Failed Expression: from < static_cast(size()) 169: **** 169: -141: [19:37:19] The provided InitialSeed is not an MCS and will be ignored -141: .[19:37:19] The provided InitialSeed is not an MCS and will be ignored -76: 0,0 0 -76: 0,1 0 -76: 1,0 0 -76: 1,1 0 -76: 2,0 0 -76: 2,1 0 -141: [19:37:19] The provided InitialSeed is not an MCS and will be ignored -141: [19:37:19] The provided InitialSeed is not an MCS and will be ignored -154/208 Test #76: testEnumeration ........................ Passed 13.80 sec -test 170 - Start 170: pyTestSGroups - -170: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/testSGroups.py" -170: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap -170: Test timeout computed to be: 1500 -141: ................. -141: ---------------------------------------------------------------------- -141: Ran 63 tests in 4.870s -141: -141: OK -155/208 Test #141: pyFMCS ................................. Passed 5.24 sec -test 171 - Start 171: pyTestThreads - -171: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/testThreads.py" -171: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap -171: Test timeout computed to be: 1500 -25: Checking against /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -171: [19:37:20] Warning: molecule is tagged as 3D, but all Z coords are zero -25: All 191 tests passed -170: ............. -170: ---------------------------------------------------------------------- -170: Ran 13 tests in 0.062s -170: -170: OK -170: Testing SubstanceGroups wrapper -156/208 Test #170: pyTestSGroups .......................... Passed 0.44 sec -test 172 - Start 172: pyTestMultithreadedMolSupplier - -172: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" -172: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap -172: Test timeout computed to be: 1500 -25: -25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... -169: .[19:37:20] +158: Best mapping +167: ...........................[16:04:03] unable to set wavy bonds for double bonds: 3 +167: .........[16:04:03] +167: +167: **** +167: Range Error +167: idx +167: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp +167: Failed Expression: 6 < 5 +167: **** +167: +169: .[16:04:03] 169: 169: **** 169: Range Error @@ -27877,7 +28980,7 @@ 169: Failed Expression: 0 < 0 169: **** 169: -169: .[19:37:20] +169: .[16:04:03] 169: 169: **** 169: Pre-condition Violation @@ -27886,7 +28989,7 @@ 169: Failed Expression: traj.dimension() == 3 169: **** 169: -169: ..[19:37:20] +169: ..[16:04:03] 169: 169: **** 169: Pre-condition Violation @@ -27895,7 +28998,7 @@ 169: Failed Expression: traj.dimension() == 3 169: **** 169: -169: .[19:37:20] +169: .[16:04:03] 169: 169: **** 169: Pre-condition Violation @@ -27904,7 +29007,7 @@ 169: Failed Expression: d_pos 169: **** 169: -169: [19:37:20] +169: [16:04:03] 169: 169: **** 169: Pre-condition Violation @@ -27913,7 +29016,7 @@ 169: Failed Expression: d_trajectory 169: **** 169: -169: .[19:37:20] +169: .[16:04:03] 169: 169: **** 169: Range Error @@ -27922,7 +29025,7 @@ 169: Failed Expression: 5 < 5 169: **** 169: -169: [19:37:20] +169: [16:04:03] 169: 169: **** 169: Range Error @@ -27931,7 +29034,7 @@ 169: Failed Expression: 10 < 10 169: **** 169: -169: .[19:37:20] +169: .[16:04:03] 169: 169: **** 169: Range Error @@ -27940,7 +29043,7 @@ 169: Failed Expression: 5 < 5 169: **** 169: -169: [19:37:20] +169: [16:04:03] 169: 169: **** 169: Pre-condition Violation @@ -27949,7 +29052,7 @@ 169: Failed Expression: d_trajectory->dimension() == 2 169: **** 169: -169: [19:37:20] +169: [16:04:03] 169: 169: **** 169: Pre-condition Violation @@ -27960,51 +29063,99 @@ 169: 169: . 169: ---------------------------------------------------------------------- -169: Ran 9 tests in 0.621s +169: Ran 9 tests in 0.559s 169: 169: OK 169: Testing Trajectory wrapper -157/208 Test #169: pyTestTrajectory ....................... Passed 0.88 sec +163/208 Test #169: pyTestTrajectory ....................... Passed 0.82 sec +test 170 + Start 170: pyTestSGroups + +170: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/testSGroups.py" +170: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap +170: Test timeout computed to be: 1500 +170: ............. +170: ---------------------------------------------------------------------- +170: Ran 13 tests in 0.033s +170: +170: OK +170: Testing SubstanceGroups wrapper +164/208 Test #170: pyTestSGroups .......................... Passed 0.28 sec +test 171 + Start 171: pyTestThreads + +171: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/testThreads.py" +171: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap +171: Test timeout computed to be: 1500 +125: .......[16:04:04] Molecule does not have explicit Hs. Consider calling AddHs() +125: .[16:04:04] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:04:04] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:04:04] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:04:04] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:04:04] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:04:04] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:04:04] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:04:04] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:04:04] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:04:04] Molecule does not have explicit Hs. Consider calling AddHs() +125: .[16:04:04] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:04:04] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:04:04] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:04:04] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:04:04] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:04:04] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:04:04] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:04:04] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:04:04] Molecule does not have explicit Hs. Consider calling AddHs() +125: [16:04:04] Molecule does not have explicit Hs. Consider calling AddHs() +125: . +125: ---------------------------------------------------------------------- +125: Ran 18 tests in 42.079s +125: +125: OK +165/208 Test #125: pyDistGeomHelpers ...................... Passed 42.65 sec +test 172 + Start 172: pyTestMultithreadedMolSupplier + +172: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" +172: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap +172: Test timeout computed to be: 1500 +171: [16:04:04] Warning: molecule is tagged as 3D, but all Z coords are zero +172: .s. +172: ---------------------------------------------------------------------- +172: Ran 3 tests in 0.090s +172: +172: OK (skipped=1) +172: Testing Smiles and SD MultithreadedMolSupplier +166/208 Test #172: pyTestMultithreadedMolSupplier ......... Passed 0.39 sec test 173 Start 173: pyTestPropertyLists 173: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/testPropertyLists.py" 173: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap 173: Test timeout computed to be: 1500 -173: [19:37:20] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -173: [19:37:20] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -173: [19:37:20] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -173: .[19:37:20] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -173: [19:37:20] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -173: [19:37:20] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -173: ..[19:37:20] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -173: [19:37:20] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -173: [19:37:20] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +173: [16:04:04] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +173: [16:04:04] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +173: [16:04:04] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +173: .[16:04:04] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +173: [16:04:04] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +173: [16:04:04] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +173: ..[16:04:04] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +173: [16:04:04] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +173: [16:04:04] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 173: . 173: ---------------------------------------------------------------------- -173: Ran 4 tests in 0.017s +173: Ran 4 tests in 0.013s 173: 173: OK -158: iterative -158/208 Test #173: pyTestPropertyLists .................... Passed 0.28 sec +167/208 Test #173: pyTestPropertyLists .................... Passed 0.26 sec test 174 Start 174: pyCDXMLTest 174: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/test_cdxml.py" 174: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap 174: Test timeout computed to be: 1500 -172: .s. -172: ---------------------------------------------------------------------- -172: Ran 3 tests in 0.144s -172: -172: OK (skipped=1) -172: Testing Smiles and SD MultithreadedMolSupplier -123: processing -123: launch :0 -123: launch :1 -123: launch :2 -123: launch :3 -159/208 Test #172: pyTestMultithreadedMolSupplier ......... Passed 0.49 sec +168/208 Test #171: pyTestThreads .......................... Passed 0.80 sec test 175 Start 175: molStandardizeTest @@ -28013,822 +29164,195 @@ 175: Test timeout computed to be: 1500 174: . 174: ---------------------------------------------------------------------- -174: Ran 1 test in 0.018s +174: Ran 1 test in 0.012s 174: 174: OK -160/208 Test #174: pyCDXMLTest ............................ Passed 0.31 sec +169/208 Test #174: pyCDXMLTest ............................ Passed 0.27 sec test 176 Start 176: molNormalizeTest 176: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest 176: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize 176: Test timeout computed to be: 1500 -155: [19:37:21] ------------------------------------- -155: [19:37:21] testing PatternHolder -176: [19:37:21] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 -176: [19:37:21] Initializing Normalizer -176: [19:37:21] Running Normalizer -176: [19:37:21] Rule applied: BrokenazidetoN=N+=N- -176: [19:37:21] Initializing Normalizer -176: [19:37:21] Running Normalizer -176: [19:37:21] Initializing Normalizer -176: [19:37:21] Running Normalizer -161/208 Test #176: molNormalizeTest ....................... Passed 0.21 sec +176: [16:04:05] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 +176: [16:04:05] Initializing Normalizer +176: [16:04:05] Running Normalizer +176: [16:04:05] Rule applied: BrokenazidetoN=N+=N- +176: [16:04:05] Initializing Normalizer +176: [16:04:05] Running Normalizer +176: [16:04:05] Initializing Normalizer +176: [16:04:05] Running Normalizer +170/208 Test #176: molNormalizeTest ....................... Passed 0.15 sec test 177 Start 177: molValidateTest 177: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest 177: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize 177: Test timeout computed to be: 1500 -162/208 Test #177: molValidateTest ........................ Passed 0.12 sec +171/208 Test #177: molValidateTest ........................ Passed 0.11 sec test 178 Start 178: molChargeTest 178: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest 178: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize 178: Test timeout computed to be: 1500 -155: [19:37:21] ------------------------------------- -155: [19:37:21] testing TautomerPatternHolder -163/208 Test #178: molChargeTest .......................... Passed 0.24 sec +172/208 Test #178: molChargeTest .......................... Passed 0.15 sec test 179 Start 179: molTautomerTest 179: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest 179: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize 179: Test timeout computed to be: 1500 -155: [19:37:21] ------------------------------------- -155: [19:37:21] testSegFaultInHolder -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[19:37:21] for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] [19:37:21] [19:37:21] [19:37:21] SMILES Parse Error: syntax errorSMILES Parse Error: syntax error while parsing: dsafsdf -155: SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[19:37:21] while parsing: dsafsdf'dsafsdf -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] [19:37:21] [19:37:21] SMILES Parse Error: syntax error while parsing: SMILES Parse Error: syntax error while parsing: SMILES Parse Error: SMILES Parse Error: syntax errordsafsdf -155: dsafsdf -155: -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf[19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: SMILES -155: [19:37:21] [19:37:21] syntax error while parsing: dsafsdf -155: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error[19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES[19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: SMILES Parse Error: syntax error while parsing: dsafsdf -155: syntax error while parsing: [19:37:21] Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: SMILES Parse Error: syntax error while parsing: dsafsdf -155: SMILES[19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '' -155: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: syntax error while parsing: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: while parsing: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: dsafsdf -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] [19:37:21] [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'SMILES Parse Error: dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdfSMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: syntax error[19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: syntax error while parsing: dsafsdf[19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: -155: SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] [19:37:21] SMILES Parse Error: syntax error[19:37:21] SMILES Parse Error: while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: syntax error while parsing: [19:37:21] [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: SMILES Parse Error: syntax errorSMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[19:37:21] ' -155: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: ' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[19:37:21] [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: SMILES Parse Error: syntax errorsyntax error while parsing: dsafsdf -155: while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: dsafsdf -155: -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:21] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:21] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [19:37:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [19:37:22] ------------------------------------- -155: [19:37:22] Results do not depend on numThreads -158: bulk -167: ...........................[19:37:22] unable to set wavy bonds for double bonds: 3 -167: .........[19:37:22] -167: -167: **** -167: Range Error -167: idx -167: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp -167: Failed Expression: 6 < 5 -167: **** -167: -179: [19:37:22] Tautomer enumeration stopped at 292 tautomers: max transforms reached -164/208 Test #175: molStandardizeTest ..................... Passed 1.93 sec +167: ...................[16:04:05] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [16:04:05] Explicit valence for atom # 6 F, 2, is greater than permitted +167: [16:04:05] Can't kekulize mol. Unkekulized atoms: 3 4 5 +167: .[16:04:05] Warning: molecule is tagged as 3D, but all Z coords are zero +167: [16:04:05] Warning: molecule is tagged as 3D, but all Z coords are zero +167: [16:04:05] Warning: molecule is tagged as 3D, but all Z coords are zero +167: [16:04:05] Warning: molecule is tagged as 3D, but all Z coords are zero +167: [16:04:05] Warning: molecule is tagged as 3D, but all Z coords are zero +167: [16:04:05] Warning: molecule is tagged as 3D, but all Z coords are zero +173/208 Test #175: molStandardizeTest ..................... Passed 1.29 sec test 180 Start 180: molStandardizeSmallTest 180: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest 180: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize 180: Test timeout computed to be: 1500 -165/208 Test #180: molStandardizeSmallTest ................ Passed 0.05 sec +179: [16:04:06] Tautomer enumeration stopped at 292 tautomers: max transforms reached +174/208 Test #180: molStandardizeSmallTest ................ Passed 0.06 sec test 181 Start 181: molFragmentTest 181: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest 181: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize 181: Test timeout computed to be: 1500 -181: [19:37:22] SMARTS Parse Error: syntax error while parsing: [Cl -181: [19:37:22] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' -166/208 Test #181: molFragmentTest ........................ Passed 0.07 sec +181: [16:04:06] SMARTS Parse Error: syntax error while parsing: [Cl +181: [16:04:06] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' +175/208 Test #181: molFragmentTest ........................ Passed 0.07 sec test 182 Start 182: molStandardizeCatchTest 182: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest 182: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize 182: Test timeout computed to be: 1500 -136: Done -136: ----------------- Test Github #781: Rendering single-atom molecules -136: file testGithub781_3.svg gave hash 4141108304U not the expected 3655151266U -136: Done -136: ----------------- Test 3 -136: file test3_1.png gave hash 457962218U not the expected 1578780280U -136: file test3_2.png gave hash 3723407046U not the expected 1100583374U -136: file test3_3.png gave hash 715516981U not the expected 2405974883U -136: file test3_3.svg gave hash 220863844U not the expected 3967096277U -136: file test3_4.png gave hash 2817418133U not the expected 3523404550U -136: file test3_4.svg gave hash 2724848547U not the expected 1410409071U -136: file test3_5.png gave hash 2019575530U not the expected 411486117U -136: file test3_6.png gave hash 946969094U not the expected 2817453573U 182: * - * - * - * m1 182: * - * - * - * m2 -136: file test3_7.png gave hash 1623443833U not the expected 285272009U 182: * - * - * - * m1 182: * - * - * - * m2 -136: Done -136: ----------------- Test Github774: upside-down drawings -182: [19:37:23] Can't kekulize mol. Unkekulized atoms: 3 7 -136: file test774_1.png gave hash 3501940912U not the expected 930347428U -182: [19:37:23] Can't kekulize mol. Unkekulized atoms: 3 8 -182: [19:37:23] Can't kekulize mol. Unkekulized atoms: 2 3 4 +182: [16:04:06] Can't kekulize mol. Unkekulized atoms: 3 7 +182: [16:04:06] Can't kekulize mol. Unkekulized atoms: 3 8 +182: [16:04:06] Can't kekulize mol. Unkekulized atoms: 2 3 4 182: =============================================================================== 182: All tests passed (240 assertions in 36 test cases) 182: -167/208 Test #182: molStandardizeCatchTest ................ Passed 0.34 sec +176/208 Test #182: molStandardizeCatchTest ................ Passed 0.31 sec test 183 Start 183: pyMolStandardize 183: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" 183: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap 183: Test timeout computed to be: 1500 -136: file test774_2.png gave hash 3395890193U not the expected 1089219024U -136: Done -136: ----------------- Test 9 (molecule legends) -136: file test9_1.svg gave hash 618149026U not the expected 3204904541U -136: Done -136: ----------------- Test Github852: Lines used to wedge bonds are too thick -136: file test852_1.png gave hash 171258688U not the expected 4140960740U -179: [19:37:23] Tautomer enumeration stopped at 292 tautomers: max transforms reached -136: file test852_2.png gave hash 3927167691U not the expected 4294133823U -136: ---------------- -136: ---------------- -136: ---------------- -136: ---------------- -136: Done -136: ----------------- Test Github860: Atom symbols in wrong order if bond comes from right -136: file test860_1.png gave hash 2949617705U not the expected 1000110983U -136: file test860_2.png gave hash 1584078969U not the expected 4079976606U -136: file test860_3.png gave hash 3063101059U not the expected 1675954369U -136: Done -136: ----------------- Test Github #910: ugly coordinates generated for peptide chains -136: Done -136: ----------------- Test Github #932: mistake in SVG for wedged bonds -136: Done -136: ----------------- Test Github #953: default color should not be cyan -136: Done -136: ----------------- Test Github #983: wedged bonds between chiral centers drawn improperly -136: Done -136: ----------------- Test Deuterium, Tritium -179: [19:37:23] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -136: Done -136: ----------------- Test crossed bonds -136: Done -136: ----------------- Testing drawing a second molecule -136: Done -136: ----------------- Testing drawing a grid of molecules -136: Done -136: ----------------- Testing drawMolecules -136: file test12_1.svg gave hash 2818547989U not the expected 459314393U -136: file test12_5.svg gave hash 816880708U not the expected 3040108534U -136: Done -136: ----------------- Test JSON Configuration -136: Done -136: ----------------- Testing github 1090: escape html characters in SVG output -136: Done -136: ----------------- Testing github 1035: overflow bug in SVG color generation -136: Done -136: ----------------- Testing github 1271: MolDraw2D not drawing anything for molecules aligned with the X or Y axes -136: Done -136: ----------------- Testing github 1322: add custom atom labels -136: Done -136: ----------------- Testing use of a black & white palette -136: Done -136: ----------------- Testing use of continuous highlighting with drawMolecules -136: Done -136: ----------------- Test 17 - Testing maximum font size -136: Done -136: ----------------- Testing github 1829: crash when drawMolecules() is called with an empty list -136: Done -136: ----------------- Testing use of fixed scales for drawing. -136: file test18_5.svg gave hash 548307340U not the expected 3983014844U -136: [19:37:23] -136: -136: **** -136: Test Assert -136: Expression Failed: -136: Violation occurred on line 3392 in file ./Code/GraphMol/MolDraw2D/test1.cpp -136: Failed Expression: drawer.fontSize() == 24 -136: **** -136: -136: terminate called after throwing an instance of 'Invar::Invariant' -136: what(): Expression Failed: -168/208 Test #136: moldraw2DTest1 .........................Subprocess aborted***Exception: 10.88 sec - ----------------- Test 1 -file test1_5.svg gave hash 3105787089U not the expected 2964125114U -file test1_6.svg gave hash 995867455U not the expected 464012122U - Done - ----------------- Test 2 -file test2_1.png gave hash 2637189532U not the expected 2505713963U -file test2_2.png gave hash 2877988061U not the expected 4058920248U - Done - ----------------- Test 4 -file test4_1.png gave hash 747479389U not the expected 1924202631U - Done - ----------------- Test 5 -file test5_1.png gave hash 1284534124U not the expected 2116545562U -file test5_2.png gave hash 1548238783U not the expected 1519942634U -file test5_3.png gave hash 2001032737U not the expected 3266389887U - Done - ----------------- Test 6 (atom labels) - Done - ----------------- Test 7 (backgrounds) -file test7_1.png gave hash 2952006174U not the expected 3331950391U -file test7_2.png gave hash 425772459U not the expected 1686496331U - Done - ----------------- Test8: PrepareMolDrawing - Done - ----------------- Test multi-threaded drawing -reading molecules -generating reference drawings -processing - launch :0 - launch :1 - launch :2 - launch :3 - Done - ----------------- Test Github #781: Rendering single-atom molecules -file testGithub781_3.svg gave hash 4141108304U not the expected 3655151266U - Done - ----------------- Test 3 -file test3_1.png gave hash 457962218U not the expected 1578780280U -file test3_2.png gave hash 3723407046U not the expected 1100583374U -file test3_3.png gave hash 715516981U not the expected 2405974883U -file test3_3.svg gave hash 220863844U not the expected 3967096277U -file test3_4.png gave hash 2817418133U not the expected 3523404550U -file test3_4.svg gave hash 2724848547U not the expected 1410409071U -file test3_5.png gave hash 2019575530U not the expected 411486117U -file test3_6.png gave hash 946969094U not the expected 2817453573U -file test3_7.png gave hash 1623443833U not the expected 285272009U - Done - ----------------- Test Github774: upside-down drawings -file test774_1.png gave hash 3501940912U not the expected 930347428U -file test774_2.png gave hash 3395890193U not the expected 1089219024U - Done - ----------------- Test 9 (molecule legends) -file test9_1.svg gave hash 618149026U not the expected 3204904541U - Done - ----------------- Test Github852: Lines used to wedge bonds are too thick -file test852_1.png gave hash 171258688U not the expected 4140960740U -file test852_2.png gave hash 3927167691U not the expected 4294133823U ----------------- ----------------- ----------------- ----------------- - Done - ----------------- Test Github860: Atom symbols in wrong order if bond comes from right -file test860_1.png gave hash 2949617705U not the expected 1000110983U -file test860_2.png gave hash 1584078969U not the expected 4079976606U -file test860_3.png gave hash 3063101059U not the expected 1675954369U - Done - ----------------- Test Github #910: ugly coordinates generated for peptide chains - Done - ----------------- Test Github #932: mistake in SVG for wedged bonds - Done - ----------------- Test Github #953: default color should not be cyan - Done - ----------------- Test Github #983: wedged bonds between chiral centers drawn improperly - Done - ----------------- Test Deuterium, Tritium - Done - ----------------- Test crossed bonds - Done - ----------------- Testing drawing a second molecule - Done - ----------------- Testing drawing a grid of molecules - Done - ----------------- Testing drawMolecules -file test12_1.svg gave hash 2818547989U not the expected 459314393U -file test12_5.svg gave hash 816880708U not the expected 3040108534U - Done - ----------------- Test JSON Configuration - Done - ----------------- Testing github 1090: escape html characters in SVG output - Done - ----------------- Testing github 1035: overflow bug in SVG color generation - Done - ----------------- Testing github 1271: MolDraw2D not drawing anything for molecules aligned with the X or Y axes - Done - ----------------- Testing github 1322: add custom atom labels - Done - ----------------- Testing use of a black & white palette - Done - ----------------- Testing use of continuous highlighting with drawMolecules - Done - ----------------- Test 17 - Testing maximum font size - Done - ----------------- Testing github 1829: crash when drawMolecules() is called with an empty list - Done - ----------------- Testing use of fixed scales for drawing. -file test18_5.svg gave hash 548307340U not the expected 3983014844U -[19:37:23] - -**** -Test Assert -Expression Failed: -Violation occurred on line 3392 in file ./Code/GraphMol/MolDraw2D/test1.cpp -Failed Expression: drawer.fontSize() == 24 -**** - -terminate called after throwing an instance of 'Invar::Invariant' - what(): Expression Failed: - +179: [16:04:06] Tautomer enumeration stopped at 292 tautomers: max transforms reached +179: [16:04:06] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +179: [16:04:07] Tautomer enumeration stopped at 70 tautomers: canceled +179: Enumeration was canceled due to timeout (50 ms) +177/208 Test #158: testRGroupDecomp ....................... Passed 13.57 sec test 184 Start 184: testScaffoldNetwork 184: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork 184: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork 184: Test timeout computed to be: 1500 -169/208 Test #171: pyTestThreads .......................... Passed 3.61 sec +183: .....[16:04:07] Tautomer enumeration stopped at 292 tautomers: max transforms reached +183: [16:04:07] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +179: 375 +179: Enumeration has completed +179: [16:04:07] Tautomer enumeration stopped at 37 tautomers: canceled +183: .[16:04:08] Tautomer enumeration stopped at 42 tautomers: canceled +183: Enumeration was canceled due to timeout (50 ms) +184: =============================================================================== +184: All tests passed (266 assertions in 18 test cases) +184: +178/208 Test #184: testScaffoldNetwork .................... Passed 1.41 sec test 185 Start 185: pyScaffoldNetwork 185: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" 185: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 185: Test timeout computed to be: 1500 -179: [19:37:23] Tautomer enumeration stopped at 43 tautomers: canceled -179: Enumeration was canceled due to timeout (50 ms) -185: ....... -185: ---------------------------------------------------------------------- -185: Ran 7 tests in 0.057s -185: -185: OK -170/208 Test #185: pyScaffoldNetwork ...................... Passed 0.38 sec +179: CN=c1cc[nH]cn1 +179: CN=c1ccnc[nH]1 +179: CNc1ccncn1 +179: res: CNc1ccncn1 +179: CN=c1cccc[nH]1 +179: CNc1ccccn1 +179: res: CNc1ccccn1 +179/208 Test #179: molTautomerTest ........................ Passed 3.78 sec test 186 Start 186: pyScaffoldNetworkPickling 186: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" 186: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 186: Test timeout computed to be: 1500 -158: bulk, no symmetry -167: ...................[19:37:24] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [19:37:24] Explicit valence for atom # 6 F, 2, is greater than permitted -167: [19:37:24] Can't kekulize mol. Unkekulized atoms: 3 4 5 -167: .[19:37:24] Warning: molecule is tagged as 3D, but all Z coords are zero -167: [19:37:24] Warning: molecule is tagged as 3D, but all Z coords are zero -167: [19:37:24] Warning: molecule is tagged as 3D, but all Z coords are zero -167: [19:37:24] Warning: molecule is tagged as 3D, but all Z coords are zero -167: [19:37:24] Warning: molecule is tagged as 3D, but all Z coords are zero -167: [19:37:24] Warning: molecule is tagged as 3D, but all Z coords are zero -186: . -186: ---------------------------------------------------------------------- -186: Ran 1 test in 0.018s -186: -186: OK -171/208 Test #186: pyScaffoldNetworkPickling .............. Passed 0.29 sec +183: Enumeration has completed +185: ....... +185: ---------------------------------------------------------------------- +185: Ran 7 tests in 0.117s +185: +185: OK +183: [16:04:09] Tautomer enumeration stopped at 41 tautomers: canceled +180/208 Test #185: pyScaffoldNetwork ...................... Passed 0.70 sec test 187 Start 187: testMolEnumerator 187: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator 187: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator 187: Test timeout computed to be: 1500 -183: .....[19:37:24] Tautomer enumeration stopped at 292 tautomers: max transforms reached -187: [19:37:24] can only enumerate SRUs with CONNECT=HT or CONNECT=HH -187: =============================================================================== -187: All tests passed (247 assertions in 12 test cases) -187: -172/208 Test #187: testMolEnumerator ...................... Passed 0.10 sec +186: . +186: ---------------------------------------------------------------------- +186: Ran 1 test in 0.021s +186: +186: OK +181/208 Test #186: pyScaffoldNetworkPickling .............. Passed 0.33 sec test 188 Start 188: pyMolEnumerator 188: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" 188: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/Wrap 188: Test timeout computed to be: 1500 -183: [19:37:24] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -179: 375 -179: Enumeration has completed -188: ... -188: ---------------------------------------------------------------------- -188: Ran 3 tests in 0.017s -188: -188: OK -173/208 Test #188: pyMolEnumerator ........................ Passed 0.28 sec +187: [16:04:09] can only enumerate SRUs with CONNECT=HT or CONNECT=HH +187: =============================================================================== +187: All tests passed (247 assertions in 12 test cases) +187: +182/208 Test #187: testMolEnumerator ...................... Passed 0.14 sec test 189 Start 189: testAbbreviations 189: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations 189: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations 189: Test timeout computed to be: 1500 -129: ............[19:37:24] Molecule does not have explicit Hs. Consider calling AddHs() -179: [19:37:24] Tautomer enumeration stopped at 47 tautomers: canceled -189: [19:37:24] SMARTS Parse Error: syntax error while parsing: *fail -189: [19:37:24] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' -189: [19:37:24] no suitable SubstanceGroups found +189: [16:04:09] SMARTS Parse Error: syntax error while parsing: *fail +189: [16:04:09] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' +189: [16:04:09] no suitable SubstanceGroups found 189: =============================================================================== 189: All tests passed (195 assertions in 12 test cases) 189: -174/208 Test #189: testAbbreviations ...................... Passed 0.06 sec +183/208 Test #189: testAbbreviations ...................... Passed 0.10 sec test 190 Start 190: pyAbbreviations 190: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" 190: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/Wrap 190: Test timeout computed to be: 1500 -183: .[19:37:24] Tautomer enumeration stopped at 40 tautomers: canceled -183: Enumeration was canceled due to timeout (50 ms) -129: [19:37:24] Molecule does not have explicit Hs. Consider calling AddHs() -129: [19:37:24] Molecule does not have explicit Hs. Consider calling AddHs() -129: [19:37:24] Molecule does not have explicit Hs. Consider calling AddHs() -129: [19:37:24] Molecule does not have explicit Hs. Consider calling AddHs() -129: [19:37:24] Molecule does not have explicit Hs. Consider calling AddHs() -129: [19:37:24] Molecule does not have explicit Hs. Consider calling AddHs() -129: [19:37:24] Molecule does not have explicit Hs. Consider calling AddHs() -129: [19:37:24] Molecule does not have explicit Hs. Consider calling AddHs() -129: [19:37:24] Molecule does not have explicit Hs. Consider calling AddHs() -129: [19:37:24] Molecule does not have explicit Hs. Consider calling AddHs() -190: ....... -190: ---------------------------------------------------------------------- -190: Ran 7 tests in 0.027s -190: -190: OK -175/208 Test #190: pyAbbreviations ........................ Passed 0.27 sec +183: ...............[16:04:10] Explicit valence for atom # 1 O, 3, is greater than permitted +183: . +183: ---------------------------------------------------------------------- +183: Ran 22 tests in 3.046s +183: +183: OK +183: done +184/208 Test #183: pyMolStandardize ....................... Passed 3.41 sec test 191 Start 191: testQuery @@ -28852,7 +29376,7 @@ 191: XOr 191: pointer and copy foo 191: Set2 -176/208 Test #191: testQuery .............................. Passed 0.01 sec +185/208 Test #191: testQuery .............................. Passed 0.03 sec test 192 Start 192: testMatCalc @@ -28904,38 +29428,32 @@ 192: 9.49496e+07 192: 2.25618e+08 192: 1.30219e+08 -177/208 Test #192: testMatCalc ............................ Passed 0.01 sec +186/208 Test #192: testMatCalc ............................ Passed 0.03 sec test 193 Start 193: pyMatCalc 193: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" 193: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap 193: Test timeout computed to be: 1500 -158: [19:37:25] Relabelling existing label -184: =============================================================================== -184: All tests passed (266 assertions in 18 test cases) -184: -178/208 Test #184: testScaffoldNetwork .................... Passed 1.73 sec +188: ... +188: ---------------------------------------------------------------------- +188: Ran 3 tests in 0.022s +188: +188: OK +187/208 Test #188: pyMolEnumerator ........................ Passed 0.55 sec test 194 Start 194: testSimDivPickers 194: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers/testSimDivPickers 194: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers 194: Test timeout computed to be: 1500 -179: CN=c1cc[nH]cn1 -179: CN=c1ccnc[nH]1 -179: CNc1ccncn1 -179: res: CNc1ccncn1 -179: CN=c1cccc[nH]1 -179: CNc1ccccn1 -179: res: CNc1ccccn1 -194: [19:37:25] ------------------------------------- -194: [19:37:25] Testing github issue 1421: MaxMinPicker picking non-existent element. -194: [19:37:25] Done -194: [19:37:25] ------------------------------------- -194: [19:37:25] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. -194: [19:37:25] Done -179/208 Test #194: testSimDivPickers ...................... Passed 0.01 sec +194: [16:04:10] ------------------------------------- +194: [16:04:10] Testing github issue 1421: MaxMinPicker picking non-existent element. +194: [16:04:10] Done +194: [16:04:10] ------------------------------------- +194: [16:04:10] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. +194: [16:04:10] Done +188/208 Test #194: testSimDivPickers ...................... Passed 0.01 sec test 195 Start 195: pickersTestsCatch @@ -28945,47 +29463,29 @@ 195: =============================================================================== 195: All tests passed (21267 assertions in 1 test case) 195: -180/208 Test #195: pickersTestsCatch ...................... Passed 0.11 sec +189/208 Test #195: pickersTestsCatch ...................... Passed 0.13 sec test 196 Start 196: pySimDivPickers 196: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/testPickers.py" 196: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers/Wrap 196: Test timeout computed to be: 1500 -158: Best mapping -181/208 Test #179: molTautomerTest ........................ Passed 3.91 sec +190: ....... +190: ---------------------------------------------------------------------- +190: Ran 7 tests in 0.055s +190: +190: OK +190/208 Test #190: pyAbbreviations ........................ Passed 0.59 sec test 197 Start 197: pyRanker 197: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/testRanker.py" 197: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap 197: Test timeout computed to be: 1500 -193: ..... -193: ---------------------------------------------------------------------- -193: Ran 5 tests in 0.480s -193: -193: OK -196: [19:37:25] the useCache argument is deprecated and ignored -182/208 Test #193: pyMatCalc .............................. Passed 0.70 sec -test 198 - Start 198: testChemicalFeatures - -198: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures -198: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures -198: Test timeout computed to be: 1500 -198: ----------------------------------------- -198: Test1 -198: Done -183/208 Test #198: testChemicalFeatures ................... Passed 0.01 sec -test 199 - Start 199: pyFeatures - -199: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/Wrap/testFeatures.py" -199: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures/Wrap -199: Test timeout computed to be: 1500 +196: [16:04:10] the useCache argument is deprecated and ignored 197: ../build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/testRanker.py:124: DeprecationWarning: Please use assertRaisesRegex instead. 197: with self.assertRaisesRegexp(Exception, ""): -197: [19:37:25] +197: [16:04:11] 197: 197: **** 197: Invariant Violation @@ -28996,53 +29496,87 @@ 197: 197: ... 197: ---------------------------------------------------------------------- -197: Ran 5 tests in 0.026s +197: Ran 5 tests in 0.052s 197: 197: OK -184/208 Test #197: pyRanker ............................... Passed 0.24 sec -test 200 - Start 200: pythonTestDbCLI +196: ...[16:04:11] the useCache argument is deprecated and ignored +196: [16:04:11] the useCache argument is deprecated and ignored +196: .[16:04:11] the useCache argument is deprecated and ignored +191/208 Test #197: pyRanker ............................... Passed 0.51 sec +test 198 + Start 198: testChemicalFeatures -200: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Projects/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/Projects" -200: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Projects -200: Test timeout computed to be: 1500 -196: ...[19:37:25] the useCache argument is deprecated and ignored -196: [19:37:25] the useCache argument is deprecated and ignored -196: .[19:37:25] the useCache argument is deprecated and ignored +198: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures +198: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures +198: Test timeout computed to be: 1500 +198: ----------------------------------------- +198: Test1 +198: Done +192/208 Test #198: testChemicalFeatures ................... Passed 0.02 sec +test 199 + Start 199: pyFeatures + +199: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/Wrap/testFeatures.py" +199: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ChemicalFeatures/Wrap +199: Test timeout computed to be: 1500 199: .. 199: ---------------------------------------------------------------------- 199: Ran 2 tests in 0.002s 199: 199: OK 199: Testing ChemicalFeatures Wrapper code: -185/208 Test #199: pyFeatures ............................. Passed 0.33 sec +193/208 Test #199: pyFeatures ............................. Passed 0.64 sec +test 200 + Start 200: pythonTestDbCLI + +200: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Projects/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/Projects" +200: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Projects +200: Test timeout computed to be: 1500 +193: ..... +193: ---------------------------------------------------------------------- +193: Ran 5 tests in 1.107s +193: +193: OK +194/208 Test #193: pyMatCalc .............................. Passed 1.64 sec test 201 Start 201: pythonTestDirRoot 201: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit" 201: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit 201: Test timeout computed to be: 1500 -183: Enumeration has completed -201: ......................... -201: ---------------------------------------------------------------------- -201: Ran 25 tests in 0.198s -201: -201: OK -183: [19:37:26] Tautomer enumeration stopped at 42 tautomers: canceled -186/208 Test #201: pythonTestDirRoot ...................... Passed 0.37 sec +196: ....... +196: ---------------------------------------------------------------------- +196: Ran 11 tests in 2.066s +196: +196: OK +195/208 Test #196: pySimDivPickers ........................ Passed 2.35 sec test 202 Start 202: pythonTestDirML 202: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/ML/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/ML" 202: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit 202: Test timeout computed to be: 1500 -155: [19:37:26] ------------------------------------- -155: [19:37:26] Results do not depend on numThreads (all same) -200: [19:37:26] INFO: Reading molecules and constructing molecular database. +200: [16:04:12] INFO: Reading molecules and constructing molecular database. 200: -200: [19:37:26] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [16:04:12] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: [19:37:26] INFO: Processing 10 molecules +200: [16:04:12] INFO: Processing 10 molecules +200: +201: ......................... +201: ---------------------------------------------------------------------- +201: Ran 25 tests in 0.765s +201: +201: OK +200: [16:04:13] INFO: Generating fingerprints and descriptors: +200: +196/208 Test #201: pythonTestDirRoot ...................... Passed 1.14 sec +test 203 + Start 203: pythonTestDirDataStructs + +203: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/DataStructs/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/DataStructs" +203: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit +203: Test timeout computed to be: 1500 +200: [16:04:13] INFO: Finished. 200: 202: EEEEEEE 202: ====================================================================== @@ -29165,40 +29699,31 @@ 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- -202: Ran 7 tests in 0.067s +202: Ran 7 tests in 0.151s 202: 202: FAILED (errors=7) -183: ...............[19:37:26] Explicit valence for atom # 1 O, 3, is greater than permitted -183: . -183: ---------------------------------------------------------------------- -183: Ran 22 tests in 3.277s -183: -183: OK -183: done -187/208 Test #183: pyMolStandardize ....................... Passed 3.61 sec -test 203 - Start 203: pythonTestDirDataStructs - -203: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/DataStructs/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/DataStructs" -203: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit -203: Test timeout computed to be: 1500 -155: [19:37:26] ------------------------------------- -155: [19:37:26] testTautomerQueries -200: [19:37:26] INFO: Generating fingerprints and descriptors: +203: ....... +203: ---------------------------------------------------------------------- +203: Ran 7 tests in 0.045s +203: +203: OK +200: [16:04:13] INFO: Reading molecules and constructing molecular database. 200: -155: [19:37:26] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... -155: [19:37:26] ------------------------------------- -155: [19:37:26] github3881 recursive smarts with rings -188/208 Test #155: substructLibraryTest ................... Passed 10.26 sec -test 204 - Start 204: pythonTestDirDbase - -204: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/Dbase/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/Dbase" -204: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit -204: Test timeout computed to be: 1500 -200: [19:37:27] INFO: Finished. +200: [16:04:13] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -25: Checking against /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +200: [16:04:13] INFO: Processing 163 molecules +200: +200: [16:04:14] INFO: done 100 +200: +200: [16:04:14] INFO: Generating fingerprints and descriptors: +200: +203: ............../build/reproducible-path/rdkit-202209.3/rdkit/DataStructs/UnitTestcBitVect.py:42: DeprecationWarning: Please use assertRaisesRegex instead. +203: with self.assertRaisesRegexp(IndexError, ""): +203: .................... +203: ---------------------------------------------------------------------- +203: Ran 34 tests in 0.014s +203: +203: OK 202: EEEEEEEEEEEE 202: ====================================================================== 202: ERROR: test10_filtering (__main__.TestCase.test10_filtering) @@ -29405,63 +29930,10 @@ 202: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 202: 202: ---------------------------------------------------------------------- -202: Ran 12 tests in 0.137s +202: Ran 12 tests in 0.117s 202: 202: FAILED (errors=12) -204: .. -204: ---------------------------------------------------------------------- -204: Ran 2 tests in 0.060s -204: -204: OK -25: All 191 tests passed -25: done -25: ------------------------------------- -25: Unit tests for all MMFF constraint terms. -203: ....... -203: ---------------------------------------------------------------------- -203: Ran 7 tests in 0.024s -203: -203: OK -25: 10.0003 -196: ....... -196: ---------------------------------------------------------------------- -196: Ran 11 tests in 1.675s -196: -196: OK -25: done -25: ------------------------------------- -25: Unit test for MMFF TorsionConstraint close to 0 degrees. -25: done -25: ------------------------------------- -25: Unit tests for copying MMFF ForceFields. -204: ........... -204: ---------------------------------------------------------------------- -204: Ran 11 tests in 0.045s -204: -204: OK -25: done -25: ------------------------------------- -25: Unit test for MMFF butane scan. -189/208 Test #196: pySimDivPickers ........................ Passed 1.93 sec -test 205 - Start 205: pythonTestDirSimDivFilters - -205: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/SimDivFilters/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/SimDivFilters" -205: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit -205: Test timeout computed to be: 1500 -204: . -204: ---------------------------------------------------------------------- -204: Ran 1 test in 0.001s -204: -204: OK -203: ............../build/reproducible-path/rdkit-202209.3/rdkit/DataStructs/UnitTestcBitVect.py:42: DeprecationWarning: Please use assertRaisesRegex instead. -203: with self.assertRaisesRegexp(IndexError, ""): 202: Traceback (most recent call last): -203: .................... -203: ---------------------------------------------------------------------- -203: Ran 34 tests in 0.006s -203: -203: OK 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestAnalyzeComposite.py", line 44, in test1_Issue163 202: res = sorted(AnalyzeComposite.ProcessIt([c1, c2], verbose=-1)) 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ @@ -29484,435 +29956,210 @@ 202: AssertionError: 0 is not true 202: 202: ---------------------------------------------------------------------- -202: Ran 1 test in 0.031s +202: Ran 1 test in 0.040s 202: 202: FAILED (failures=1) -204: ../build/reproducible-path/rdkit-202209.3/rdkit/Dbase/UnitTestDbUtils.py:96: DeprecationWarning: Please use assertRaisesRegex instead. -204: with self.assertRaisesRegexp(IndexError, ""): -204: ............. -204: ---------------------------------------------------------------------- -204: Ran 15 tests in 0.057s -204: -204: OK -200: [19:37:27] INFO: Reading molecules and constructing molecular database. -200: -200: [19:37:27] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt -200: -200: [19:37:27] INFO: Processing 163 molecules -200: -204: ...... -204: ---------------------------------------------------------------------- -204: Ran 6 tests in 0.005s -204: -204: OK +167: ...............[16:04:14] +167: +167: **** +167: Pre-condition Violation +167: no owner +167: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h +167: Failed Expression: dp_mol +167: **** +167: +167: [16:04:14] +167: +167: **** +167: Pre-condition Violation +167: no owner +167: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h +167: Failed Expression: dp_mol +167: **** +167: +167: [16:04:14] +167: +167: **** +167: Pre-condition Violation +167: no owner +167: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h +167: Failed Expression: dp_mol +167: **** +167: +167: [16:04:14] +167: +167: **** +167: Pre-condition Violation +167: no owner +167: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h +167: Failed Expression: dp_mol +167: **** +167: +167: [16:04:14] +167: +167: **** +167: Pre-condition Violation +167: no owner +167: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h +167: Failed Expression: dp_mol +167: **** +167: 203: ..... 203: ---------------------------------------------------------------------- -203: Ran 5 tests in 0.019s +203: Ran 5 tests in 0.130s 203: 203: OK -190/208 Test #204: pythonTestDirDbase ..................... Passed 0.81 sec -test 206 - Start 206: pythonTestDirVLib - -206: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/VLib/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/VLib" -206: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit -206: Test timeout computed to be: 1500 -191/208 Test #205: pythonTestDirSimDivFilters ............. Passed 0.37 sec -test 207 - Start 207: pythonTestSping - -207: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/sping" -207: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit -207: Test timeout computed to be: 1500 +167: .....[16:04:14] +167: +167: **** +167: Range Error +167: atomIdx1 +167: Violation occurred on line 331 in file ./Code/GraphMol/RWMol.cpp +167: Failed Expression: 0 < 0 +167: **** +167: +167: ......[16:04:14] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +167: [16:04:14] ERROR: Smiles parse error on line 0 +167: [16:04:14] ERROR: Cannot create molecule from : 'c1ccccc' +167: [16:04:14] SMILES Parse Error: extra open parentheses for input: 'C(C' +167: [16:04:14] ERROR: Smiles parse error on line 3 +167: [16:04:14] ERROR: Cannot create molecule from : 'C(C' +167: [16:04:14] Explicit valence for atom # 1 C, 5, is greater than permitted +167: [16:04:14] ERROR: Could not sanitize molecule on line 6 +167: [16:04:14] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +167: [16:04:14] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +167: [16:04:14] ERROR: Smiles parse error on line 0 +167: [16:04:14] ERROR: Cannot create molecule from : 'c1ccccc' +167: [16:04:14] SMILES Parse Error: extra open parentheses for input: 'C(C' +167: [16:04:14] ERROR: Smiles parse error on line 3 +167: [16:04:14] ERROR: Cannot create molecule from : 'C(C' +167: [16:04:14] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' +167: [16:04:14] ERROR: Smiles parse error on line 6 +167: [16:04:14] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' +167: [16:04:14] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [16:04:14] ERROR: Could not sanitize molecule ending on line 21 +167: [16:04:14] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +167: [16:04:14] ERROR: EOF hit while reading atoms +167: [16:04:14] ERROR: moving to the beginning of the next molecule +167: [16:04:14] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [16:04:14] ERROR: Could not sanitize molecule ending on line 21 +167: [16:04:14] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +167: [16:04:14] ERROR: EOF hit while reading atoms +167: [16:04:14] ERROR: moving to the beginning of the next molecule 202: ... 202: ---------------------------------------------------------------------- -202: Ran 3 tests in 0.003s +202: Ran 3 tests in 0.002s +202: +202: OK +167: ....[16:04:15] +167: +167: **** +167: Pre-condition Violation +167: RingInfo not initialized +167: Violation occurred on line 169 in file ./Code/GraphMol/RingInfo.cpp +167: Failed Expression: df_init +167: **** +167: +167: ......[16:04:15] +167: +167: **** +167: Range Error +167: idx +167: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp +167: Failed Expression: 3 < 1 +167: **** +167: +167: ..[16:04:15] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +167: .................[16:04:15] SMILES Parse Error: unclosed ring for input: 'C1CC' +167: ......[16:04:15] WARNING: not removing hydrogen atom without neighbors +167: [16:04:15] WARNING: not removing hydrogen atom with dummy atom neighbors +167: [16:04:15] WARNING: not removing hydrogen atom with wedged bond +167: [16:04:15] WARNING: not removing hydrogen atom without neighbors +167: [16:04:15] WARNING: not removing hydrogen atom with dummy atom neighbors +202: ........ +202: ---------------------------------------------------------------------- +202: Ran 8 tests in 0.001s 202: 202: OK -25: done -192/208 Test #25: testMMFFForceField ..................... Passed 22.70 sec -test 208 - Start 208: pythonTestDirChem - -208: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/Chem" "--buildType" "None" -208: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem -208: Test timeout computed to be: 1500 -200: [19:37:27] INFO: done 100 -200: -149: VS001: PASSED -149: VS002: PASSED -149: VS003: PASSED -149: VS004: PASSED -149: VS005: PASSED -149: VS006: PASSED -149: VS007: PASSED -149: VS008: PASSED -149: VS009: PASSED -149: VS010: PASSED -149: VS011: PASSED -149: VS012: PASSED -149: VS013: PASSED -149: VS014: PASSED -149: VS015: PASSED -149: VS016: PASSED -149: VS017: PASSED -149: VS018: PASSED -149: VS019: PASSED -149: VS020: PASSED -149: VS021: PASSED -149: VS022: PASSED -149: VS023: PASSED -149: VS024: PASSED -149: VS025: PASSED -149: VS026: PASSED -149: VS027: PASSED -149: VS028: PASSED -149: VS029: PASSED -149: VS030: PASSED -149: VS031: PASSED -149: VS032: PASSED -149: VS033: PASSED -149: VS034: PASSED -149: VS035: PASSED -149: VS036: PASSED -149: VS037: PASSED -149: VS038: PASSED -149: VS039: PASSED -149: VS040: PASSED -149: VS041: PASSED -149: VS042: PASSED -149: VS043: PASSED -149: VS044: PASSED -149: VS045: PASSED -149: VS046: PASSED -149: VS047: PASSED -149: VS048: PASSED -149: VS049: PASSED -149: VS050: PASSED -149: VS051: PASSED -149: VS052: PASSED -149: VS053: PASSED -149: VS054: PASSED -149: VS055: PASSED -149: VS056: PASSED -149: VS057: PASSED -149: VS058: PASSED -149: VS059: PASSED -149: VS060: PASSED -149: VS061: PASSED -149: VS062: PASSED -149: VS063: PASSED -149: VS064: PASSED -149: VS065: PASSED -149: VS066: PASSED -149: VS067: PASSED -149: VS068: PASSED -149: VS069: PASSED -149: VS070: PASSED -149: VS071: PASSED -149: VS072: PASSED -149: VS073: PASSED -149: VS074: PASSED -149: VS075: PASSED -149: VS076: PASSED -149: VS077: PASSED -149: VS078: PASSED -149: VS079: PASSED -149: VS080: PASSED -149: VS081: PASSED -149: VS082: PASSED -149: VS083: PASSED -149: VS084: PASSED -149: VS085: PASSED -149: VS086: PASSED -149: VS087: PASSED -149: VS088: PASSED -149: VS089: PASSED -149: VS090: PASSED -149: VS091: PASSED -149: VS092: PASSED -149: VS093: PASSED -149: VS094: PASSED -149: VS095: PASSED -149: VS096: PASSED -149: VS097: PASSED -149: VS098: PASSED -149: VS099: PASSED -149: VS100: PASSED -149: VS101: PASSED -149: VS102: PASSED -149: VS103: PASSED -149: VS104: PASSED -149: VS105: PASSED -149: VS106: PASSED -149: VS107: PASSED -149: VS108: PASSED -149: VS109: PASSED -149: VS110: PASSED -149: VS111: PASSED -149: VS112: PASSED -149: VS113: PASSED -149: VS114: PASSED -149: VS115: PASSED -149: VS116: PASSED -149: VS117: PASSED -149: VS118: PASSED -149: VS119: PASSED -149: VS120: PASSED -149: VS121: PASSED -149: VS122: PASSED -149: VS123: PASSED -149: VS124: PASSED -149: VS125: PASSED -149: VS126: PASSED -149: VS127: PASSED -149: VS128: PASSED -149: VS129: PASSED -149: VS130: PASSED -149: VS131: PASSED -149: VS132: PASSED -149: VS133: PASSED -149: VS134: PASSED -149: VS135: PASSED -149: VS136: PASSED -149: VS137: PASSED -149: VS138: PASSED -149: VS139: PASSED -149: VS140: PASSED -149: VS141: PASSED -149: VS142: PASSED -149: VS143: PASSED -149: VS144: PASSED -149: VS145: PASSED -149: VS146: PASSED -149: VS147: PASSED -149: VS148: PASSED -149: VS149: PASSED -149: VS150: PASSED -149: VS151: PASSED -149: VS152: PASSED -149: VS153: PASSED -149: VS154: PASSED -149: VS155: PASSED -149: VS156: PASSED -149: VS157: PASSED -149: VS158: PASSED -149: VS159: PASSED -149: VS160: PASSED -149: VS161: PASSED -149: VS162: PASSED -149: VS163: PASSED -149: VS164: PASSED -149: VS165: PASSED -149: VS166: PASSED -149: VS167: PASSED -149: VS168: PASSED -149: VS169: PASSED -149: VS170: PASSED -149: VS171: PASSED -149: VS172: PASSED -149: VS173: PASSED -149: VS174: PASSED -149: VS175: PASSED -149: VS176: PASSED -149: VS177: PASSED -149: VS178: PASSED -149: VS179: PASSED -149: VS180: PASSED -149: VS181: PASSED -149: VS182: PASSED -149: VS183: PASSED -149: VS184: PASSED -149: VS185: PASSED -149: VS186: PASSED -149: VS187: PASSED -149: VS188: PASSED -149: VS189: PASSED -149: VS190: PASSED -149: VS191: PASSED -149: VS192: PASSED -149: VS193: PASSED -149: VS194: PASSED -149: VS195: PASSED -149: VS196: PASSED -149: VS197: PASSED -149: VS198: PASSED -149: VS199: PASSED -149: VS200: PASSED -149: VS201: PASSED -149: VS202: PASSED -149: VS203: PASSED -149: VS204: PASSED -149: VS205: PASSED -149: VS206: PASSED -149: VS207: PASSED -149: VS208: PASSED -149: VS209: PASSED -149: VS210: PASSED -149: VS211: PASSED -149: VS212: PASSED -149: VS213: PASSED -149: VS214: PASSED -149: VS215: PASSED -149: VS216: PASSED -149: VS217: PASSED -149: VS218: PASSED -149: VS219: PASSED -149: VS220: PASSED -149: VS221: PASSED -149: VS222: PASSED -149: VS223: PASSED -149: VS224: PASSED -149: VS225: PASSED -149: VS226: PASSED -149: VS227: PASSED -149: VS228: PASSED -149: VS229: PASSED -149: VS230: PASSED -149: VS231: PASSED -149: VS232: PASSED -149: VS233: PASSED -149: VS234: PASSED -149: VS235: PASSED -149: VS236: PASSED -149: VS237: PASSED -149: VS238: PASSED -149: VS239: PASSED -149: VS240: PASSED -149: VS241: PASSED -149: VS242: PASSED -149: VS243: PASSED -149: VS244: PASSED -149: VS245: PASSED -149: VS246: PASSED -149: VS247: PASSED -149: VS248: PASSED -149: VS249: PASSED -149: VS250: PASSED -149: VS251: PASSED -149: VS252: PASSED -149: VS253: PASSED -149: VS254: PASSED -149: VS255: PASSED -149: VS256: PASSED -149: VS257: PASSED -149: VS258: PASSED -149: VS259: PASSED -149: VS260: PASSED -149: VS261: PASSED -149: VS262: PASSED -149: VS263: PASSED -149: VS264: PASSED -149: VS265: PASSED -149: VS266: PASSED -149: VS267: PASSED -149: VS268: PASSED -149: VS269: PASSED -149: VS270: PASSED -149: VS271: PASSED -149: VS272: PASSED -149: VS273: PASSED -149: VS274: PASSED -149: VS275: PASSED -149: VS276: PASSED -149: VS277: PASSED -149: VS278: PASSED -149: VS279: PASSED -149: VS280: PASSED -149: VS281: PASSED -149: VS282: PASSED -149: VS283: PASSED -149: VS284: PASSED -149: VS285: PASSED -149: VS286: PASSED -149: VS287: PASSED -149: VS288: PASSED -149: VS289: PASSED -149: VS290: PASSED -149: VS291: PASSED -149: VS292: PASSED -149: VS293: PASSED -149: VS294: PASSED -149: VS295: PASSED -149: VS296: PASSED -149: VS297: PASSED -149: VS298: PASSED -149: VS299: PASSED -149: VS300: PASSED -149: Check finished: 0 molecules failed. -149: Failed: -193/208 Test #149: pyCIPLabelsValidation .................. Passed 12.01 sec -206: ............. -206: ---------------------------------------------------------------------- -206: Ran 13 tests in 0.011s -206: -206: OK 203: ....... 203: ---------------------------------------------------------------------- -203: Ran 7 tests in 0.001s +203: Ran 7 tests in 0.002s 203: 203: OK -200: [19:37:27] INFO: Generating fingerprints and descriptors: -200: -129: ...[19:37:27] Molecule does not have explicit Hs. Consider calling AddHs() -129: [19:37:27] Molecule does not have explicit Hs. Consider calling AddHs() -129: [19:37:27] Molecule does not have explicit Hs. Consider calling AddHs() -129: [19:37:27] Molecule does not have explicit Hs. Consider calling AddHs() -129: [19:37:27] Molecule does not have explicit Hs. Consider calling AddHs() -194/208 Test #203: pythonTestDirDataStructs ............... Passed 1.13 sec -202: ........ +167: .....[16:04:15] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [16:04:15] Can't kekulize mol. Unkekulized atoms: 0 1 2 +167: .[16:04:15] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [16:04:15] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [16:04:15] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [16:04:15] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [16:04:15] Can't kekulize mol. Unkekulized atoms: 0 1 2 +167: [16:04:15] Can't kekulize mol. Unkekulized atoms: 0 1 2 +167: [16:04:15] Can't kekulize mol. Unkekulized atoms: 0 1 2 +197/208 Test #203: pythonTestDirDataStructs ............... Passed 2.43 sec +test 204 + Start 204: pythonTestDirDbase + +204: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/Dbase/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/Dbase" +204: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit +204: Test timeout computed to be: 1500 +167: ..........[16:04:15] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +167: [16:04:15] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +167: .[16:04:15] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +167: [16:04:15] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +167: ..[16:04:15] SMILES Parse Error: syntax error while parsing: error +167: [16:04:15] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' +167: [16:04:15] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' +167: [16:04:15] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' +167: [16:04:15] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' +167: ...........[16:04:15] SMILES Parse Error: syntax error while parsing: garbage_0 +167: [16:04:15] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' +167: [16:04:15] SMILES Parse Error: syntax error while parsing: garbage_2 +167: [16:04:15] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' +167: [16:04:15] SMILES Parse Error: syntax error while parsing: garbage_4 +167: [16:04:15] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' +167: ......... +167: ---------------------------------------------------------------------- +167: Ran 228 tests in 16.970s +167: +167: OK +167: 16 +167: supplier: +167: supplier: +167: supplier: +198/208 Test #167: pyGraphMolWrap ......................... Passed 17.41 sec +test 205 + Start 205: pythonTestDirSimDivFilters + +205: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/SimDivFilters/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/SimDivFilters" +205: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit +205: Test timeout computed to be: 1500 +204: .. +204: ---------------------------------------------------------------------- +204: Ran 2 tests in 0.126s +204: +204: OK +202: .... 202: ---------------------------------------------------------------------- -202: Ran 8 tests in 0.001s +202: Ran 4 tests in 0.178s 202: 202: OK -129: ... -129: ---------------------------------------------------------------------- -129: Ran 18 tests in 16.467s -129: -129: OK -129: Testing MolAlign Wrappers -195/208 Test #129: pyMolAlign ............................. Passed 16.76 sec -206: ........... +199/208 Test #205: pythonTestDirSimDivFilters ............. Passed 0.64 sec +test 206 + Start 206: pythonTestDirVLib + +206: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/VLib/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/VLib" +206: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit +206: Test timeout computed to be: 1500 +204: ........... +204: ---------------------------------------------------------------------- +204: Ran 11 tests in 0.126s +204: +204: OK +206: ............. 206: ---------------------------------------------------------------------- -206: Ran 11 tests in 0.055s +206: Ran 13 tests in 0.011s 206: 206: OK -196/208 Test #206: pythonTestDirVLib ...................... Passed 0.59 sec -208: ....... -208: ---------------------------------------------------------------------- -208: Ran 7 tests in 0.135s -208: -208: OK -207: .. -207: ---------------------------------------------------------------------- -207: Ran 2 tests in 0.236s -207: -207: OK -202: .... -202: ---------------------------------------------------------------------- -202: Ran 4 tests in 0.155s -202: -202: OK -197/208 Test #207: pythonTestSping ........................ Passed 0.70 sec -198/208 Test #158: testRGroupDecomp ....................... Passed 11.39 sec -157: ......[19:37:28] -157: -157: **** -157: Pre-condition Violation -157: RingInfo not initialized -157: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp -157: Failed Expression: df_init -157: **** -157: -157: [19:37:28] -157: -157: **** -157: Pre-condition Violation -157: RingInfo not initialized -157: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp -157: Failed Expression: df_init -157: **** -157: 202: E.EEE 202: ====================================================================== 202: ERROR: test1_basics (__main__.TestCase.test1_basics) @@ -29971,28 +30218,14 @@ 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- -202: Ran 5 tests in 0.003s +202: Ran 5 tests in 0.004s 202: 202: FAILED (errors=4) -208: ...... -208: ---------------------------------------------------------------------- -208: Ran 6 tests in 0.055s -208: -208: OK -208: ....[19:37:28] -208: -208: **** -208: Pre-condition Violation -208: valence not defined for atoms not associated with molecules -208: Violation occurred on line 422 in file ./Code/GraphMol/Atom.cpp -208: Failed Expression: dp_mol -208: **** -208: -208: . -208: ---------------------------------------------------------------------- -208: Ran 5 tests in 0.008s -208: -208: OK +204: . +204: ---------------------------------------------------------------------- +204: Ran 1 test in 0.001s +204: +204: OK 202: .......E. 202: ====================================================================== 202: ERROR: test_RandomizeActivities (__main__.TestCase.test_RandomizeActivities) @@ -30005,29 +30238,50 @@ 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- -202: Ran 9 tests in 0.004s +202: Ran 9 tests in 0.005s 202: 202: FAILED (errors=1) +204: ../build/reproducible-path/rdkit-202209.3/rdkit/Dbase/UnitTestDbUtils.py:96: DeprecationWarning: Please use assertRaisesRegex instead. +204: with self.assertRaisesRegexp(IndexError, ""): +204: ............. +204: ---------------------------------------------------------------------- +204: Ran 15 tests in 0.200s +204: +204: OK 202: ............ 202: ---------------------------------------------------------------------- 202: Ran 12 tests in 0.003s 202: 202: OK -208: .... -208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.011s -208: -208: OK +206: ........... +206: ---------------------------------------------------------------------- +206: Ran 11 tests in 0.065s +206: +206: OK +200/208 Test #206: pythonTestDirVLib ...................... Passed 0.88 sec +test 207 + Start 207: pythonTestSping + +207: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/sping" +207: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit +207: Test timeout computed to be: 1500 +204: ...... +204: ---------------------------------------------------------------------- +204: Ran 6 tests in 0.009s +204: +204: OK +201/208 Test #204: pythonTestDirDbase ..................... Passed 1.73 sec +test 208 + Start 208: pythonTestDirChem + +208: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/Chem" "--buildType" "None" +208: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem +208: Test timeout computed to be: 1500 202: ..... 202: ---------------------------------------------------------------------- -202: Ran 5 tests in 0.020s +202: Ran 5 tests in 0.028s 202: 202: OK -208: .. -208: ---------------------------------------------------------------------- -208: Ran 2 tests in 0.014s -208: -208: OK 202: ********************************************************************** 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 208, in __main__.SplitDbData 202: Failed example: @@ -30221,151 +30475,86 @@ 202: 8 of 16 in __main__.SplitDbData 202: 6 of 22 in __main__.SplitIndices 202: ***Test Failed*** 14 failures. -208: ...................... -208: ---------------------------------------------------------------------- -208: Ran 22 tests in 0.032s -208: -208: OK 202: !!! TEST FAILURE: python UnitTestFilter.py {} 202: !!! TEST FAILURE: python UnitTestMLData.py {} 202: !!! TEST FAILURE: python SplitData.py {} +208: ....... +208: ---------------------------------------------------------------------- +208: Ran 7 tests in 0.147s +208: +208: OK +207: .. +207: ---------------------------------------------------------------------- +207: Ran 2 tests in 0.253s +207: +207: OK 202: . 202: ---------------------------------------------------------------------- 202: Ran 1 test in 0.000s 202: 202: OK +202/208 Test #207: pythonTestSping ........................ Passed 0.97 sec 202: ...... 202: ---------------------------------------------------------------------- 202: Ran 6 tests in 0.002s 202: 202: OK -208: .....s..........E......ss -208: ====================================================================== -208: ERROR: testIpc (__main__.TestCase.testIpc) +208: ...... 208: ---------------------------------------------------------------------- -208: Traceback (most recent call last): -208: File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/UnitTestGraphDescriptors_2.py", line 112, in testIpc -208: Ipc = GraphDescriptors.Ipc(m, forceDMat=1) -208: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -208: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/GraphDescriptors.py", line 124, in Ipc -208: cPoly = abs(Graphs.CharacteristicPolynomial(mol, adjMat)) -208: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -208: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/Graphs.py", line 43, in CharacteristicPolynomial -208: res = numpy.zeros(nAtoms + 1, numpy.float) -208: ^^^^^^^^^^^ -208: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ -208: raise AttributeError(__former_attrs__[attr]) -208: AttributeError: module 'numpy' has no attribute 'float'. -208: `np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here. -208: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: -208: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations +208: Ran 6 tests in 0.059s +208: +208: OK +127: --------------------------------- +127: test getO3AForProbeConfs +127: +127: *********************************************************** +203/208 Test #127: testO3AAlign ........................... Passed 55.20 sec +208: ....[16:04:18] +208: +208: **** +208: Pre-condition Violation +208: valence not defined for atoms not associated with molecules +208: Violation occurred on line 422 in file ./Code/GraphMol/Atom.cpp +208: Failed Expression: dp_mol +208: **** 208: +208: . 208: ---------------------------------------------------------------------- -208: Ran 25 tests in 0.165s +208: Ran 5 tests in 0.017s 208: -208: FAILED (errors=1, skipped=3) +208: OK 202: .... 202: ---------------------------------------------------------------------- -202: Ran 4 tests in 0.131s +202: Ran 4 tests in 0.246s 202: 202: OK -208: ..s +200: [16:04:18] INFO: Finished. +200: +208: .... 208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.191s +208: Ran 4 tests in 0.012s 208: -208: OK (skipped=1) +208: OK 202: ...... 202: ---------------------------------------------------------------------- -202: Ran 6 tests in 0.013s +202: Ran 6 tests in 0.020s 202: 202: OK +208: .. +208: ---------------------------------------------------------------------- +208: Ran 2 tests in 0.012s +208: +208: OK 202: .. 202: ---------------------------------------------------------------------- -202: Ran 2 tests in 0.098s +202: Ran 2 tests in 0.128s 202: 202: OK -167: ...............[19:37:31] -167: -167: **** -167: Pre-condition Violation -167: no owner -167: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h -167: Failed Expression: dp_mol -167: **** -167: -167: [19:37:31] -167: -167: **** -167: Pre-condition Violation -167: no owner -167: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h -167: Failed Expression: dp_mol -167: **** -167: -167: [19:37:31] -167: -167: **** -167: Pre-condition Violation -167: no owner -167: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h -167: Failed Expression: dp_mol -167: **** -167: -167: [19:37:31] -167: -167: **** -167: Pre-condition Violation -167: no owner -167: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h -167: Failed Expression: dp_mol -167: **** -167: -167: [19:37:31] -167: -167: **** -167: Pre-condition Violation -167: no owner -167: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h -167: Failed Expression: dp_mol -167: **** -167: -167: .....[19:37:31] -167: -167: **** -167: Range Error -167: atomIdx1 -167: Violation occurred on line 331 in file ./Code/GraphMol/RWMol.cpp -167: Failed Expression: 0 < 0 -167: **** -167: -167: ......[19:37:31] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -167: [19:37:31] ERROR: Smiles parse error on line 0 -167: [19:37:31] ERROR: Cannot create molecule from : 'c1ccccc' -167: [19:37:31] SMILES Parse Error: extra open parentheses for input: 'C(C' -167: [19:37:31] ERROR: Smiles parse error on line 3 -167: [19:37:31] ERROR: Cannot create molecule from : 'C(C' -167: [19:37:31] Explicit valence for atom # 1 C, 5, is greater than permitted -167: [19:37:31] ERROR: Could not sanitize molecule on line 6 -167: [19:37:31] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -167: [19:37:31] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -167: [19:37:31] ERROR: Smiles parse error on line 0 -167: [19:37:31] ERROR: Cannot create molecule from : 'c1ccccc' -167: [19:37:31] SMILES Parse Error: extra open parentheses for input: 'C(C' -167: [19:37:31] ERROR: Smiles parse error on line 3 -167: [19:37:31] ERROR: Cannot create molecule from : 'C(C' -167: [19:37:31] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' -167: [19:37:31] ERROR: Smiles parse error on line 6 -167: [19:37:31] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' -167: [19:37:31] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [19:37:31] ERROR: Could not sanitize molecule ending on line 21 -167: [19:37:31] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -167: [19:37:31] ERROR: EOF hit while reading atoms -167: [19:37:31] ERROR: moving to the beginning of the next molecule -167: [19:37:31] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [19:37:31] ERROR: Could not sanitize molecule ending on line 21 -167: [19:37:31] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -167: [19:37:31] ERROR: EOF hit while reading atoms -167: [19:37:31] ERROR: moving to the beginning of the next molecule +208: ...................... +208: ---------------------------------------------------------------------- +208: Ran 22 tests in 0.039s +208: +208: OK 202: ........E. 202: ====================================================================== 202: ERROR: test8RandomForest (__main__.TestCase.test8RandomForest) @@ -30382,92 +30571,50 @@ 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- -202: Ran 10 tests in 0.010s +202: Ran 10 tests in 0.012s 202: 202: FAILED (errors=1) -167: ....[19:37:31] -167: -167: **** -167: Pre-condition Violation -167: RingInfo not initialized -167: Violation occurred on line 169 in file ./Code/GraphMol/RingInfo.cpp -167: Failed Expression: df_init -167: **** -167: -167: ......[19:37:31] -167: -167: **** -167: Range Error -167: idx -167: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp -167: Failed Expression: 3 < 1 -167: **** -167: -167: ..[19:37:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -167: .................[19:37:31] SMILES Parse Error: unclosed ring for input: 'C1CC' -167: ......[19:37:31] WARNING: not removing hydrogen atom without neighbors -167: [19:37:31] WARNING: not removing hydrogen atom with dummy atom neighbors -167: [19:37:31] WARNING: not removing hydrogen atom with wedged bond -167: [19:37:31] WARNING: not removing hydrogen atom without neighbors -167: [19:37:31] WARNING: not removing hydrogen atom with dummy atom neighbors +208: .....s..........E......ss +208: ====================================================================== +208: ERROR: testIpc (__main__.TestCase.testIpc) +208: ---------------------------------------------------------------------- +208: Traceback (most recent call last): +208: File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/UnitTestGraphDescriptors_2.py", line 112, in testIpc +208: Ipc = GraphDescriptors.Ipc(m, forceDMat=1) +208: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +208: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/GraphDescriptors.py", line 124, in Ipc +208: cPoly = abs(Graphs.CharacteristicPolynomial(mol, adjMat)) +208: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +208: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/Graphs.py", line 43, in CharacteristicPolynomial +208: res = numpy.zeros(nAtoms + 1, numpy.float) +208: ^^^^^^^^^^^ +208: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ +208: raise AttributeError(__former_attrs__[attr]) +208: AttributeError: module 'numpy' has no attribute 'float'. +208: `np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here. +208: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: +208: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations +208: +208: ---------------------------------------------------------------------- +208: Ran 25 tests in 0.180s +208: +208: FAILED (errors=1, skipped=3) 202: ..... 202: ---------------------------------------------------------------------- -202: Ran 5 tests in 0.111s +202: Ran 5 tests in 0.150s 202: 202: OK 202: !!! TEST FAILURE: python UnitTestQuantTree.py {} -157: ............ -157: ---------------------------------------------------------------------- -157: Ran 18 tests in 14.038s -157: -157: OK -157: Testing atom rings -157: testing bond rings -157: searching atom rings -157: searching bond rings -157: done -199/208 Test #157: pySubstructLibrary ..................... Passed 14.34 sec -200: [19:37:31] INFO: Finished. -200: 202: .. 202: ---------------------------------------------------------------------- -202: Ran 2 tests in 0.003s +202: Ran 2 tests in 0.004s 202: 202: OK -167: .....[19:37:31] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [19:37:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 -167: .[19:37:31] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [19:37:31] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [19:37:31] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [19:37:31] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [19:37:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 -167: [19:37:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 -167: [19:37:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 -167: ..........[19:37:31] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -167: [19:37:31] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -167: .[19:37:31] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -167: [19:37:31] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -167: ..[19:37:31] SMILES Parse Error: syntax error while parsing: error -167: [19:37:31] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' -167: [19:37:31] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' -167: [19:37:31] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' -167: [19:37:31] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' -167: ...........[19:37:31] SMILES Parse Error: syntax error while parsing: garbage_0 -167: [19:37:31] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' -167: [19:37:31] SMILES Parse Error: syntax error while parsing: garbage_2 -167: [19:37:31] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' -167: [19:37:31] SMILES Parse Error: syntax error while parsing: garbage_4 -167: [19:37:31] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' -167: ......... -167: ---------------------------------------------------------------------- -167: Ran 228 tests in 13.093s -167: -167: OK -167: 643 -167: supplier: -167: supplier: -167: supplier: -200/208 Test #167: pyGraphMolWrap ......................... Passed 13.48 sec +208: ..s +208: ---------------------------------------------------------------------- +208: Ran 3 tests in 0.219s +208: +208: OK (skipped=1) 202: ....Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Descriptors/MoleculeDescriptors.py", line 88, in CalcDescriptors 202: res[i] = fn(mol) @@ -30494,25 +30641,15 @@ 202: RuntimeError: Incomplete pickle support (__getstate_manages_dict__ not set) 202: 202: ---------------------------------------------------------------------- -202: Ran 5 tests in 0.011s +202: Ran 5 tests in 0.018s 202: 202: FAILED (errors=1) -208: ................................... -208: ---------------------------------------------------------------------- -208: Ran 35 tests in 1.056s -208: -208: OK 202: ... 202: ---------------------------------------------------------------------- -202: Ran 3 tests in 0.008s +202: Ran 3 tests in 0.012s 202: 202: OK 202: !!! TEST FAILURE: python UnitTestMolDescriptors.py {} -208: .... -208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.025s -208: -208: OK 202: EEE 202: ====================================================================== 202: ERROR: test0CorrMat (__main__.TestCase.test0CorrMat) @@ -30543,24 +30680,24 @@ 202: 202: FAILED (errors=3) 202: !!! TEST FAILURE: python UnitTestCorrMatGen.py {} -208: . -208: ---------------------------------------------------------------------- -208: Ran 1 test in 0.016s -208: -208: OK -208: ....... +208: ................................... 208: ---------------------------------------------------------------------- -208: Ran 7 tests in 0.040s +208: Ran 35 tests in 1.058s 208: 208: OK 202: ...... 202: ---------------------------------------------------------------------- -202: Ran 6 tests in 0.337s +202: Ran 6 tests in 0.577s 202: 202: OK -208: ... +208: .... +208: ---------------------------------------------------------------------- +208: Ran 4 tests in 0.028s +208: +208: OK +208: . 208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.046s +208: Ran 1 test in 0.018s 208: 208: OK 202: ...EE.. @@ -30581,44 +30718,47 @@ 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- -202: Ran 7 tests in 0.064s +202: Ran 7 tests in 0.102s 202: 202: FAILED (errors=2) 202: !!! TEST FAILURE: python UnitTestPackage.py {} +208: ....... +208: ---------------------------------------------------------------------- +208: Ran 7 tests in 0.064s +208: +208: OK 202: .... 202: ---------------------------------------------------------------------- -202: Ran 4 tests in 0.013s +202: Ran 4 tests in 0.016s 202: 202: OK -29: [19:37:33] Finished -29: [19:37:33] ------------------------------------- -29: [19:37:33] Test github1843: RWMol.clear() should not destroy ring pointer. -29: [19:37:33] Finished -201/208 Test #29: graphmolTest1 .......................... Passed 28.58 sec +208: ... +208: ---------------------------------------------------------------------- +208: Ran 3 tests in 0.060s +208: +208: OK 208: .ss.ss....... 208: ---------------------------------------------------------------------- -208: Ran 13 tests in 1.147s +208: Ran 13 tests in 1.856s 208: 208: OK (skipped=4) -127: --------------------------------- -127: test O3A multithreading bug -127: -127: --------------------------------- -127: testCrippenO3A multithreading -127: -127: generating reference data -208: [19:37:34] Molecule does not have explicit Hs. Consider calling AddHs() -208: .[19:37:34] Molecule does not have explicit Hs. Consider calling AddHs() -127: processing -127: launch :0 -127: launch :1 -127: launch :2 -127: launch :3 +208: [16:04:25] Molecule does not have explicit Hs. Consider calling AddHs() +208: .[16:04:25] Molecule does not have explicit Hs. Consider calling AddHs() 202: ..... 202: ---------------------------------------------------------------------- -202: Ran 5 tests in 2.028s +202: Ran 5 tests in 3.704s 202: 202: OK +200: .........[16:04:27] INFO: Reading molecules and constructing molecular database. +200: +200: [16:04:27] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: +200: [16:04:27] INFO: Processing 10 molecules +200: +200: [16:04:27] INFO: Generating fingerprints and descriptors: +200: +200: [16:04:27] INFO: Finished. +200: 202: .... 202: ---------------------------------------------------------------------- 202: Ran 4 tests in 0.002s @@ -30629,36 +30769,9 @@ 202: Ran 4 tests in 0.001s 202: 202: OK -125: .......[19:37:36] Molecule does not have explicit Hs. Consider calling AddHs() -125: .[19:37:36] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:36] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:36] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:36] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:36] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:36] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:36] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:36] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:36] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:36] Molecule does not have explicit Hs. Consider calling AddHs() -125: .[19:37:36] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:36] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:36] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:36] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:36] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:36] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:36] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:36] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:36] Molecule does not have explicit Hs. Consider calling AddHs() -125: [19:37:36] Molecule does not have explicit Hs. Consider calling AddHs() -125: . -125: ---------------------------------------------------------------------- -125: Ran 18 tests in 25.522s -125: -125: OK -202/208 Test #125: pyDistGeomHelpers ...................... Passed 25.79 sec 202: .... 202: ---------------------------------------------------------------------- -202: Ran 4 tests in 0.004s +202: Ran 4 tests in 0.005s 202: 202: OK 202: !!! TEST FAILURE: python UnitTestBuildComposite.py {} @@ -30669,7 +30782,7 @@ 202: !!! TEST FAILURE: python test_list.py {'dir': 'Descriptors'} 202: !!! TEST FAILURE: python test_list.py {'dir': 'InfoTheory'} 202: !!! TEST FAILURE: python test_list.py {'dir': 'ModelPackage'} -203/208 Test #202: pythonTestDirML ........................***Failed 10.06 sec +204/208 Test #202: pythonTestDirML ........................***Failed 15.01 sec EEEEEEE ====================================================================== ERROR: test1_basics (__main__.TestCase.test1_basics) @@ -30791,7 +30904,7 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 7 tests in 0.067s +Ran 7 tests in 0.151s FAILED (errors=7) EEEEEEEEEEEE @@ -31000,7 +31113,7 @@ https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations ---------------------------------------------------------------------- -Ran 12 tests in 0.137s +Ran 12 tests in 0.117s FAILED (errors=12) Traceback (most recent call last): @@ -31026,12 +31139,12 @@ AssertionError: 0 is not true ---------------------------------------------------------------------- -Ran 1 test in 0.031s +Ran 1 test in 0.040s FAILED (failures=1) ... ---------------------------------------------------------------------- -Ran 3 tests in 0.003s +Ran 3 tests in 0.002s OK ........ @@ -31041,7 +31154,7 @@ OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.155s +Ran 4 tests in 0.178s OK E.EEE @@ -31102,7 +31215,7 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 5 tests in 0.003s +Ran 5 tests in 0.004s FAILED (errors=4) .......E. @@ -31117,7 +31230,7 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 9 tests in 0.004s +Ran 9 tests in 0.005s FAILED (errors=1) ............ @@ -31127,7 +31240,7 @@ OK ..... ---------------------------------------------------------------------- -Ran 5 tests in 0.020s +Ran 5 tests in 0.028s OK ********************************************************************** @@ -31338,17 +31451,17 @@ OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.131s +Ran 4 tests in 0.246s OK ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.013s +Ran 6 tests in 0.020s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.098s +Ran 2 tests in 0.128s OK ........E. @@ -31367,18 +31480,18 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 10 tests in 0.010s +Ran 10 tests in 0.012s FAILED (errors=1) ..... ---------------------------------------------------------------------- -Ran 5 tests in 0.111s +Ran 5 tests in 0.150s OK !!! TEST FAILURE: python UnitTestQuantTree.py {} .. ---------------------------------------------------------------------- -Ran 2 tests in 0.003s +Ran 2 tests in 0.004s OK ....Traceback (most recent call last): @@ -31407,12 +31520,12 @@ RuntimeError: Incomplete pickle support (__getstate_manages_dict__ not set) ---------------------------------------------------------------------- -Ran 5 tests in 0.011s +Ran 5 tests in 0.018s FAILED (errors=1) ... ---------------------------------------------------------------------- -Ran 3 tests in 0.008s +Ran 3 tests in 0.012s OK !!! TEST FAILURE: python UnitTestMolDescriptors.py {} @@ -31448,7 +31561,7 @@ !!! TEST FAILURE: python UnitTestCorrMatGen.py {} ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.337s +Ran 6 tests in 0.577s OK ...EE.. @@ -31469,18 +31582,18 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 7 tests in 0.064s +Ran 7 tests in 0.102s FAILED (errors=2) !!! TEST FAILURE: python UnitTestPackage.py {} .... ---------------------------------------------------------------------- -Ran 4 tests in 0.013s +Ran 4 tests in 0.016s OK ..... ---------------------------------------------------------------------- -Ran 5 tests in 2.028s +Ran 5 tests in 3.704s OK .... @@ -31495,7 +31608,7 @@ OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.004s +Ran 4 tests in 0.005s OK !!! TEST FAILURE: python UnitTestBuildComposite.py {} @@ -31507,107 +31620,100 @@ !!! TEST FAILURE: python test_list.py {'dir': 'InfoTheory'} !!! TEST FAILURE: python test_list.py {'dir': 'ModelPackage'} -200: .........[19:37:37] INFO: Reading molecules and constructing molecular database. -200: -200: [19:37:37] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt -200: -200: [19:37:37] INFO: Processing 10 molecules -200: -200: [19:37:37] INFO: Generating fingerprints and descriptors: -200: -200: [19:37:37] INFO: Finished. +200: [16:04:27] INFO: Reading molecules and constructing molecular database. 200: -200: [19:37:38] INFO: Reading molecules and constructing molecular database. +200: [16:04:27] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: [19:37:38] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [16:04:27] INFO: Processing 10 molecules 200: -200: [19:37:38] INFO: Processing 10 molecules +200: [16:04:28] INFO: Generating fingerprints and descriptors: 200: -200: [19:37:38] INFO: Generating fingerprints and descriptors: +200: [16:04:28] INFO: Finished. 200: -200: [19:37:38] INFO: Finished. +200: [16:04:28] INFO: Reading molecules and constructing molecular database. 200: -200: [19:37:38] INFO: Reading molecules and constructing molecular database. +200: [16:04:28] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: [19:37:38] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [16:04:28] INFO: Processing 10 molecules 200: -200: [19:37:38] INFO: Processing 10 molecules +200: [16:04:28] INFO: Generating fingerprints and descriptors: 200: -200: [19:37:38] INFO: Generating fingerprints and descriptors: +200: [16:04:28] INFO: Finished. 200: -200: [19:37:38] INFO: Finished. +200: [16:04:29] INFO: Reading molecules and constructing molecular database. 200: -200: [19:37:39] INFO: Reading molecules and constructing molecular database. +200: [16:04:29] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: [19:37:39] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [16:04:29] INFO: Generating fingerprints and descriptors: 200: -200: [19:37:39] INFO: Generating fingerprints and descriptors: +200: [16:04:29] INFO: Finished. 200: -200: [19:37:39] INFO: Finished. +200: [16:04:30] INFO: Reading molecules and constructing molecular database. 200: -200: [19:37:39] INFO: Reading molecules and constructing molecular database. +200: [16:04:30] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: [19:37:39] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [16:04:30] INFO: Generating fingerprints and descriptors: 200: -200: [19:37:39] INFO: Generating fingerprints and descriptors: +200: [16:04:30] INFO: Finished. 200: -200: [19:37:39] INFO: Finished. +200: .[16:04:30] INFO: Guessing that mol format is 'sdf'. Use --molFormat argument if this is wrong. 200: -200: .[19:37:40] INFO: Guessing that mol format is 'sdf'. Use --molFormat argument if this is wrong. +200: [16:04:30] INFO: Reading molecules and constructing molecular database. 200: -200: [19:37:40] INFO: Reading molecules and constructing molecular database. +200: [16:04:30] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: [19:37:40] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [16:04:30] INFO: Processing 163 molecules 200: -200: [19:37:40] INFO: Processing 163 molecules +200: [16:04:31] INFO: done 100 200: -200: [19:37:40] INFO: done 100 +200: [16:04:31] INFO: Generating fingerprints and descriptors: 200: -200: [19:37:40] INFO: Generating fingerprints and descriptors: +200: [16:04:31] INFO: Finished. 200: -200: [19:37:41] INFO: Finished. +200: .[16:04:32] INFO: Reading molecules and constructing molecular database. 200: -200: .[19:37:42] INFO: Reading molecules and constructing molecular database. +200: [16:04:32] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: [19:37:42] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [16:04:32] INFO: Processing 10 molecules 200: -200: [19:37:42] INFO: Processing 10 molecules +200: [16:04:32] INFO: Generating fingerprints and descriptors: 200: -200: [19:37:42] INFO: Generating fingerprints and descriptors: +200: [16:04:32] INFO: Finished. 200: -200: [19:37:42] INFO: Finished. +200: [16:04:33] INFO: Reading molecules and constructing molecular database. 200: -200: [19:37:42] INFO: Reading molecules and constructing molecular database. +200: [16:04:33] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: [19:37:42] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [16:04:33] INFO: Processing 10 molecules 200: -200: [19:37:42] INFO: Processing 10 molecules +200: [16:04:33] INFO: Generating fingerprints and descriptors: 200: -200: [19:37:42] INFO: Generating fingerprints and descriptors: -200: -200: [19:37:43] INFO: Finished. +200: [16:04:33] INFO: Finished. 200: 200: . 200: ---------------------------------------------------------------------- -200: Ran 12 tests in 17.045s +200: Ran 12 tests in 22.034s 200: 200: OK -204/208 Test #200: pythonTestDbCLI ........................ Passed 17.35 sec -5: [19:37:45] Finished: testMultipleTimes() -5: [19:37:45] +205/208 Test #200: pythonTestDbCLI ........................ Passed 22.28 sec +5: [16:04:36] Finished: testMultipleTimes() +5: [16:04:36] 5: ----------------------------------------- -205/208 Test #5: testConcurrentQueue .................... Passed 40.02 sec -127: --------------------------------- -127: test getO3AForProbeConfs -127: -127: *********************************************************** -206/208 Test #127: testO3AAlign ........................... Passed 34.32 sec -208: .........F........[19:38:01] WARNING: More than one matching pattern found - picking one +206/208 Test #5: testConcurrentQueue .................... Passed 103.92 sec +123: [16:05:11] done +123: CNC[C@H]1CC[C@H](C[NH3+])CC1 +208: .........F........[16:05:20] WARNING: More than one matching pattern found - picking one 208: -208: [19:38:01] WARNING: More than one matching pattern found - picking one +208: [16:05:20] WARNING: More than one matching pattern found - picking one 208: -208: .[19:38:01] WARNING: More than one matching pattern found - picking one +208: .[16:05:20] WARNING: More than one matching pattern found - picking one 208: +123: C1=NC[C@]2(CN3CC[C@@H]2C3)O1 +123: O=C(O)[C@@H]1[C@H](C(=O)O)[C@H]2CC[C@@H]1O2 +123: O=C(CCc1ccccc1)OC[C@H]1C[C@@H]2O[C@H]1[C@H]1C(=O)OC(=O)[C@H]12 +123: Cn1cc(C2=NC[C@]3(CN4CC[C@@H]3C4)O2)c2ccccc21 +123: Nc1ncnc2c1ncn2[C@@H]1C=C(CO)[C@@H](O)[C@H]1O +123: CO[C@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 208: ... 208: ====================================================================== 208: FAIL: testEnumerateStereoisomersRandomSamplingShouldBeDeterministicAndPortable (__main__.TestCase.testEnumerateStereoisomersRandomSamplingShouldBeDeterministicAndPortable) @@ -31616,19 +31722,21 @@ 208: File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/UnitTestMol3D.py", line 244, in testEnumerateStereoisomersRandomSamplingShouldBeDeterministicAndPortable 208: self.assertEqual(smiles, expected) 208: AssertionError: Items in the first set but not the second: -208: 'C/C(F)=C/[C@@H](Cl)/C=C(\\Br)[C@@H](N)I' 208: 'C/C(F)=C/[C@@H](Cl)/C=C(/Br)[C@@H](N)I' +208: 'C/C(F)=C/[C@@H](Cl)/C=C(\\Br)[C@@H](N)I' 208: Items in the second set but not the first: 208: 'C/C(F)=C/[C@@H](Cl)/C=C(\\Br)[C@H](N)I' 208: 'C/C(F)=C\\[C@H](Cl)/C=C(\\Br)[C@H](N)I' 208: 208: ---------------------------------------------------------------------- -208: Ran 23 tests in 29.691s +208: Ran 23 tests in 58.579s 208: 208: FAILED (failures=1) -208: {'C/C(F)=C\\[C@@H](C)Cl', 'C/C(F)=C/[C@@H](C)Cl', 'C/C(F)=C\\[C@H](C)Cl', 'C/C(F)=C/[C@H](C)Cl'} -208: {'C/C(F)=C\\[C@@H](C)Cl', 'C/C(F)=C/[C@@H](C)Cl', 'C/C(F)=C\\[C@H](C)Cl', 'C/C(F)=C/[C@H](C)Cl'} -208: {'F[C@H](Cl)[C@@H](F)Cl', 'F[C@@H](Cl)[C@@H](F)Cl', 'F[C@H](Cl)[C@H](F)Cl'} +208: {'C/C(F)=C\\[C@H](C)Cl', 'C/C(F)=C/[C@H](C)Cl', 'C/C(F)=C\\[C@@H](C)Cl', 'C/C(F)=C/[C@@H](C)Cl'} +208: {'C/C(F)=C\\[C@H](C)Cl', 'C/C(F)=C/[C@H](C)Cl', 'C/C(F)=C\\[C@@H](C)Cl', 'C/C(F)=C/[C@@H](C)Cl'} +208: {'F[C@H](Cl)[C@H](F)Cl', 'F[C@@H](Cl)[C@@H](F)Cl', 'F[C@H](Cl)[C@@H](F)Cl'} +123: CO[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O +123: CCS[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 208: .....E.. 208: ====================================================================== 208: ERROR: test7ScoreMolecules (__main__.TestCase.test7ScoreMolecules) @@ -31648,9 +31756,10 @@ 208: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 208: 208: ---------------------------------------------------------------------- -208: Ran 8 tests in 0.088s +208: Ran 8 tests in 0.118s 208: 208: FAILED (errors=1) +123: CCCCC[C@H](O)/C=C/[C@@]1(F)[C@H](O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)OC 208: Traceback (most recent call last): 208: File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/UnitTestDescriptors.py", line 57, in testBadAtomHandling 208: v = fn(m) @@ -31683,10 +31792,11 @@ 208: `np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here. 208: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 208: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations -208: F..[19:38:07] WARNING: not removing hydrogen atom without neighbors -208: [19:38:07] WARNING: not removing hydrogen atom without neighbors -208: [19:38:07] WARNING: not removing hydrogen atom without neighbors -208: ....[19:38:07] WARNING: not removing hydrogen atom without neighbors +123: CCCCC[C@@H](O)/C=C/[C@@]1(F)[C@H](C/C=C\CCCC(=O)OC)[C@H](O)C[C@@H]1O +208: F..[16:05:28] WARNING: not removing hydrogen atom without neighbors +208: [16:05:28] WARNING: not removing hydrogen atom without neighbors +208: [16:05:28] WARNING: not removing hydrogen atom without neighbors +208: ....[16:05:28] WARNING: not removing hydrogen atom without neighbors 208: ...... 208: ====================================================================== 208: FAIL: testBadAtomHandling (__main__.TestCase.testBadAtomHandling) @@ -31743,51 +31853,55 @@ 208: AssertionError: SMILES: CCC; Descriptor: Ipc 208: 208: ---------------------------------------------------------------------- -208: Ran 14 tests in 2.553s +208: Ran 14 tests in 3.598s 208: 208: FAILED (failures=2) +123: CNC(=O)Oc1cccc2c1OC[C@@H]1CCN(C)[C@H]21 +123: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 208: .... 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 1.019s +208: Ran 4 tests in 1.500s 208: 208: OK -123: [19:38:08] done 208: ...... 208: ---------------------------------------------------------------------- -208: Ran 6 tests in 0.269s +208: Ran 6 tests in 0.341s 208: 208: OK +123: CN1CC[C@H]2COc3c(O)cccc3[C@H]21 +123: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2 208: .......:1: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. 208: antibiotics = antibiotics.append({'Smiles':'CC1(C(N2C(S1)C(C2=O)NC(=O)CC3=CC=CC=C3)C(=O)O)C', 208: :1: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. 208: antibiotics = antibiotics.append({ 208: :1: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. 208: antibiotics = antibiotics.append({ +123: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 +123: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O 208: .......s..s........ 208: ---------------------------------------------------------------------- -208: Ran 26 tests in 1.701s +208: Ran 26 tests in 2.593s 208: 208: OK (skipped=2) -123: CNC[C@H]1CC[C@H](C[NH3+])CC1 -123: C1=NC[C@]2(CN3CC[C@@H]2C3)O1 -123: O=C(O)[C@@H]1[C@H](C(=O)O)[C@H]2CC[C@@H]1O2 -123: O=C(CCc1ccccc1)OC[C@H]1C[C@@H]2O[C@H]1[C@H]1C(=O)OC(=O)[C@H]12 -123: Cn1cc(C2=NC[C@]3(CN4CC[C@@H]3C4)O2)c2ccccc21 -123: Nc1ncnc2c1ncn2[C@@H]1C=C(CO)[C@@H](O)[C@H]1O -123: CO[C@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O -123: CO[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O -123: CCS[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O -123: CCCCC[C@H](O)/C=C/[C@@]1(F)[C@H](O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)OC -123: CCCCC[C@@H](O)/C=C/[C@@]1(F)[C@H](C/C=C\CCCC(=O)OC)[C@H](O)C[C@@H]1O -208: .............F[19:38:19] WARNING: More than one matching pattern found - picking one +123: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O +123: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O +123: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 +123: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 +123: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 +123: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 +123: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 +123: CC(=O)OC1=C(Sc2ccccc2)C[C@H]2Cc3cc4cccc(O)c4c(O)c3C(=O)[C@H]2C1 +123: Nc1ncnc2c1ncn2[C@@H]1C[C@H](CO)[C@@H](O)C1 +123: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 +208: .............F[16:05:49] WARNING: More than one matching pattern found - picking one 208: -208: [19:38:19] WARNING: More than one matching pattern found - picking one +208: [16:05:49] WARNING: More than one matching pattern found - picking one 208: -123: CNC(=O)Oc1cccc2c1OC[C@@H]1CCN(C)[C@H]21 -208: ..[19:38:19] Molecule does not have explicit Hs. Consider calling AddHs() -208: [19:38:19] Molecule does not have explicit Hs. Consider calling AddHs() -208: [19:38:19] Molecule does not have explicit Hs. Consider calling AddHs() -208: [19:38:19] Molecule does not have explicit Hs. Consider calling AddHs() +123: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 +208: ..[16:05:49] Molecule does not have explicit Hs. Consider calling AddHs() +208: [16:05:49] Molecule does not have explicit Hs. Consider calling AddHs() +208: [16:05:49] Molecule does not have explicit Hs. Consider calling AddHs() +208: [16:05:49] Molecule does not have explicit Hs. Consider calling AddHs() 208: ......... 208: ====================================================================== 208: FAIL: FindBRICSBonds (rdkit.Chem.BRICS) @@ -31816,292 +31930,286 @@ 208: 208: 208: ---------------------------------------------------------------------- -208: Ran 25 tests in 7.872s +208: Ran 25 tests in 14.241s 208: 208: FAILED (failures=1) 208: .. 208: ---------------------------------------------------------------------- -208: Ran 2 tests in 0.040s +208: Ran 2 tests in 0.056s 208: 208: OK -123: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 -123: CN1CC[C@H]2COc3c(O)cccc3[C@H]21 -123: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2 +123: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] 208: ..s... 208: ---------------------------------------------------------------------- -208: Ran 6 tests in 0.627s +208: Ran 6 tests in 0.904s 208: 208: OK (skipped=1) -208: ..[19:38:21] WARNING: not removing hydrogen atom without neighbors -208: .[19:38:21] WARNING: not removing hydrogen atom without neighbors -208: .[19:38:21] WARNING: no name column found on line 1 -208: [19:38:21] WARNING: no name column found on line 2 -208: [19:38:21] WARNING: no name column found on line 3 -208: [19:38:21] WARNING: no name column found on line 4 -208: [19:38:21] WARNING: no name column found on line 5 -208: [19:38:21] WARNING: no name column found on line 6 -208: [19:38:21] WARNING: no name column found on line 7 -208: [19:38:21] WARNING: no name column found on line 8 -208: [19:38:21] WARNING: no name column found on line 9 -208: [19:38:21] WARNING: no name column found on line 10 -208: [19:38:21] WARNING: no name column found on line 11 -208: [19:38:21] WARNING: no name column found on line 12 -208: [19:38:21] WARNING: no name column found on line 13 -208: [19:38:21] WARNING: no name column found on line 14 -208: [19:38:21] WARNING: no name column found on line 15 -208: [19:38:21] WARNING: no name column found on line 16 -208: [19:38:21] WARNING: no name column found on line 17 -208: [19:38:21] WARNING: no name column found on line 18 -208: [19:38:21] WARNING: no name column found on line 19 -208: [19:38:21] WARNING: no name column found on line 20 -208: [19:38:21] WARNING: no name column found on line 21 -208: [19:38:21] WARNING: no name column found on line 22 -208: [19:38:21] WARNING: no name column found on line 23 -208: [19:38:21] WARNING: no name column found on line 24 -208: [19:38:21] WARNING: no name column found on line 25 -208: [19:38:21] WARNING: no name column found on line 26 -208: [19:38:21] WARNING: no name column found on line 27 -208: [19:38:21] WARNING: no name column found on line 28 -208: [19:38:21] WARNING: no name column found on line 29 -208: [19:38:21] WARNING: no name column found on line 30 -208: [19:38:21] WARNING: no name column found on line 31 -208: [19:38:21] WARNING: no name column found on line 32 -208: [19:38:21] WARNING: no name column found on line 33 -208: [19:38:21] WARNING: no name column found on line 34 -208: [19:38:21] WARNING: no name column found on line 35 -208: [19:38:21] WARNING: no name column found on line 36 -208: [19:38:21] WARNING: no name column found on line 37 -208: [19:38:21] WARNING: no name column found on line 38 -208: [19:38:21] WARNING: no name column found on line 39 -208: [19:38:21] WARNING: no name column found on line 40 -208: [19:38:21] WARNING: no name column found on line 41 -208: [19:38:21] WARNING: no name column found on line 42 -208: [19:38:21] WARNING: no name column found on line 43 -208: [19:38:21] WARNING: no name column found on line 44 -208: [19:38:21] WARNING: no name column found on line 45 -208: [19:38:21] WARNING: no name column found on line 46 -208: [19:38:21] WARNING: no name column found on line 47 -208: [19:38:21] WARNING: no name column found on line 48 -208: [19:38:21] WARNING: no name column found on line 49 -208: [19:38:21] WARNING: no name column found on line 50 -208: [19:38:21] WARNING: no name column found on line 51 -208: [19:38:21] WARNING: no name column found on line 52 -208: [19:38:21] WARNING: no name column found on line 53 -208: [19:38:21] WARNING: no name column found on line 54 -208: [19:38:21] WARNING: no name column found on line 55 -208: [19:38:21] WARNING: no name column found on line 56 -208: [19:38:21] WARNING: no name column found on line 57 -208: [19:38:21] WARNING: no name column found on line 58 -208: [19:38:21] WARNING: no name column found on line 59 -208: [19:38:21] WARNING: no name column found on line 60 -208: [19:38:21] WARNING: no name column found on line 61 -208: [19:38:21] WARNING: no name column found on line 62 -208: [19:38:21] WARNING: no name column found on line 63 -208: [19:38:21] WARNING: no name column found on line 64 -208: [19:38:21] WARNING: no name column found on line 65 -208: [19:38:21] WARNING: no name column found on line 66 -208: [19:38:21] WARNING: no name column found on line 67 -208: [19:38:21] WARNING: no name column found on line 68 -208: [19:38:21] WARNING: no name column found on line 69 -208: [19:38:21] WARNING: no name column found on line 70 -208: [19:38:21] WARNING: no name column found on line 71 -208: [19:38:21] WARNING: no name column found on line 72 -208: [19:38:21] WARNING: no name column found on line 73 -208: [19:38:21] WARNING: no name column found on line 74 -208: [19:38:21] WARNING: no name column found on line 75 -208: [19:38:21] WARNING: no name column found on line 76 -208: [19:38:21] WARNING: no name column found on line 77 -208: [19:38:21] WARNING: no name column found on line 78 -208: [19:38:21] WARNING: no name column found on line 79 -208: [19:38:21] WARNING: no name column found on line 80 -208: [19:38:21] WARNING: no name column found on line 81 -208: [19:38:21] WARNING: no name column found on line 82 -208: [19:38:21] WARNING: no name column found on line 83 -208: [19:38:21] WARNING: no name column found on line 84 -208: [19:38:21] WARNING: no name column found on line 85 -208: [19:38:21] WARNING: no name column found on line 86 -208: [19:38:21] WARNING: no name column found on line 87 -208: [19:38:21] WARNING: no name column found on line 88 -208: [19:38:21] WARNING: no name column found on line 89 -208: [19:38:21] WARNING: no name column found on line 90 -208: [19:38:21] WARNING: no name column found on line 91 -208: [19:38:21] WARNING: no name column found on line 92 -208: [19:38:21] WARNING: no name column found on line 93 -208: [19:38:21] WARNING: no name column found on line 94 -208: [19:38:21] WARNING: no name column found on line 95 -208: [19:38:21] WARNING: no name column found on line 96 -208: [19:38:21] WARNING: no name column found on line 97 -208: [19:38:21] WARNING: no name column found on line 98 -208: [19:38:21] WARNING: no name column found on line 99 -208: [19:38:21] WARNING: no name column found on line 100 -208: [19:38:21] WARNING: no name column found on line 101 -208: [19:38:21] WARNING: no name column found on line 102 -208: [19:38:21] WARNING: no name column found on line 103 -208: [19:38:21] WARNING: no name column found on line 104 -208: [19:38:21] WARNING: no name column found on line 105 -208: [19:38:21] WARNING: no name column found on line 106 -208: [19:38:21] WARNING: no name column found on line 107 -208: [19:38:21] WARNING: no name column found on line 108 -208: [19:38:21] WARNING: no name column found on line 109 -208: [19:38:21] WARNING: no name column found on line 110 -208: [19:38:21] WARNING: no name column found on line 111 -208: [19:38:21] WARNING: no name column found on line 112 -208: [19:38:21] WARNING: no name column found on line 113 -208: [19:38:21] WARNING: no name column found on line 114 -208: [19:38:21] WARNING: no name column found on line 115 -208: [19:38:21] WARNING: no name column found on line 116 -208: [19:38:21] WARNING: no name column found on line 117 -208: [19:38:21] WARNING: no name column found on line 118 -208: [19:38:21] WARNING: no name column found on line 119 -208: [19:38:21] WARNING: no name column found on line 120 -208: [19:38:21] WARNING: no name column found on line 121 -208: [19:38:21] WARNING: no name column found on line 122 -208: [19:38:21] WARNING: no name column found on line 123 -208: [19:38:21] WARNING: no name column found on line 124 -208: [19:38:21] WARNING: no name column found on line 125 -208: [19:38:21] WARNING: no name column found on line 126 -208: [19:38:21] WARNING: no name column found on line 127 -208: [19:38:21] WARNING: no name column found on line 128 -208: [19:38:21] WARNING: no name column found on line 129 -208: [19:38:21] WARNING: no name column found on line 130 -208: [19:38:21] WARNING: no name column found on line 131 -208: [19:38:21] WARNING: no name column found on line 132 -208: [19:38:21] WARNING: no name column found on line 133 -208: [19:38:21] WARNING: no name column found on line 134 -208: [19:38:21] WARNING: no name column found on line 135 -208: [19:38:21] WARNING: no name column found on line 136 -208: [19:38:21] WARNING: no name column found on line 137 -208: [19:38:21] WARNING: no name column found on line 138 -208: [19:38:21] WARNING: no name column found on line 139 -208: [19:38:21] WARNING: no name column found on line 140 -208: [19:38:21] WARNING: no name column found on line 141 -208: [19:38:21] WARNING: no name column found on line 142 -208: [19:38:21] WARNING: no name column found on line 143 -208: [19:38:21] WARNING: no name column found on line 144 -208: [19:38:21] WARNING: no name column found on line 145 -208: [19:38:21] WARNING: no name column found on line 146 -208: [19:38:21] WARNING: no name column found on line 147 -208: [19:38:21] WARNING: no name column found on line 148 -208: [19:38:21] WARNING: no name column found on line 149 -208: [19:38:21] WARNING: no name column found on line 150 -208: [19:38:21] WARNING: no name column found on line 151 -208: [19:38:21] WARNING: no name column found on line 152 -208: [19:38:21] WARNING: no name column found on line 153 -208: [19:38:21] WARNING: no name column found on line 154 -208: [19:38:21] WARNING: no name column found on line 155 -208: [19:38:21] WARNING: no name column found on line 156 -208: [19:38:21] WARNING: no name column found on line 157 -208: [19:38:21] WARNING: no name column found on line 158 -208: [19:38:21] WARNING: no name column found on line 159 -208: [19:38:21] WARNING: no name column found on line 160 -208: [19:38:21] WARNING: no name column found on line 161 -208: [19:38:21] WARNING: no name column found on line 162 -208: [19:38:21] WARNING: no name column found on line 163 -208: [19:38:21] WARNING: no name column found on line 164 -208: [19:38:21] WARNING: no name column found on line 165 -208: [19:38:21] WARNING: no name column found on line 166 -208: [19:38:21] WARNING: no name column found on line 167 -208: [19:38:21] WARNING: no name column found on line 168 -208: [19:38:21] WARNING: no name column found on line 169 -208: [19:38:21] WARNING: no name column found on line 170 -208: [19:38:21] WARNING: no name column found on line 171 -208: [19:38:21] WARNING: no name column found on line 172 -208: [19:38:21] WARNING: no name column found on line 173 -208: [19:38:21] WARNING: no name column found on line 174 -208: [19:38:21] WARNING: no name column found on line 175 -208: [19:38:21] WARNING: no name column found on line 176 -208: [19:38:21] WARNING: no name column found on line 177 -208: [19:38:21] WARNING: no name column found on line 178 -208: [19:38:21] WARNING: no name column found on line 179 -208: [19:38:21] WARNING: no name column found on line 180 -208: [19:38:21] WARNING: no name column found on line 181 -208: [19:38:21] WARNING: no name column found on line 182 -208: [19:38:21] WARNING: no name column found on line 183 -208: [19:38:21] WARNING: no name column found on line 184 -208: [19:38:21] WARNING: no name column found on line 185 -208: [19:38:21] WARNING: no name column found on line 186 -208: [19:38:21] WARNING: no name column found on line 187 -208: [19:38:21] WARNING: no name column found on line 188 -208: [19:38:21] WARNING: no name column found on line 189 -208: [19:38:21] WARNING: no name column found on line 190 -208: [19:38:21] WARNING: no name column found on line 191 -208: [19:38:21] WARNING: no name column found on line 192 -208: [19:38:21] WARNING: no name column found on line 193 -208: [19:38:21] WARNING: no name column found on line 194 -208: [19:38:21] WARNING: no name column found on line 195 -208: [19:38:21] WARNING: no name column found on line 196 -208: [19:38:21] WARNING: no name column found on line 197 -208: [19:38:21] WARNING: no name column found on line 198 -208: [19:38:21] WARNING: no name column found on line 199 -208: [19:38:21] WARNING: no name column found on line 200 -208: [19:38:21] WARNING: no name column found on line 201 -208: [19:38:21] WARNING: no name column found on line 202 -208: [19:38:21] WARNING: no name column found on line 203 -208: [19:38:21] WARNING: no name column found on line 204 -208: [19:38:21] WARNING: no name column found on line 205 -208: [19:38:21] WARNING: no name column found on line 206 -208: [19:38:21] WARNING: no name column found on line 207 -208: [19:38:21] WARNING: no name column found on line 208 -208: [19:38:21] WARNING: no name column found on line 209 -208: [19:38:21] WARNING: no name column found on line 210 -208: [19:38:21] WARNING: no name column found on line 211 -208: [19:38:21] WARNING: no name column found on line 212 -208: [19:38:21] WARNING: no name column found on line 213 -208: [19:38:21] WARNING: no name column found on line 214 -208: [19:38:21] WARNING: no name column found on line 215 -208: [19:38:21] WARNING: no name column found on line 216 +208: ..[16:05:51] WARNING: not removing hydrogen atom without neighbors +208: .[16:05:51] WARNING: not removing hydrogen atom without neighbors +208: .[16:05:51] WARNING: no name column found on line 1 +208: [16:05:51] WARNING: no name column found on line 2 +208: [16:05:51] WARNING: no name column found on line 3 +208: [16:05:51] WARNING: no name column found on line 4 +208: [16:05:51] WARNING: no name column found on line 5 +208: [16:05:51] WARNING: no name column found on line 6 +208: [16:05:51] WARNING: no name column found on line 7 +208: [16:05:51] WARNING: no name column found on line 8 +208: [16:05:51] WARNING: no name column found on line 9 +208: [16:05:51] WARNING: no name column found on line 10 +208: [16:05:51] WARNING: no name column found on line 11 +208: [16:05:51] WARNING: no name column found on line 12 +208: [16:05:51] WARNING: no name column found on line 13 +208: [16:05:51] WARNING: no name column found on line 14 +208: [16:05:51] WARNING: no name column found on line 15 +208: [16:05:51] WARNING: no name column found on line 16 +208: [16:05:51] WARNING: no name column found on line 17 +208: [16:05:51] WARNING: no name column found on line 18 +208: [16:05:51] WARNING: no name column found on line 19 +208: [16:05:51] WARNING: no name column found on line 20 +208: [16:05:51] WARNING: no name column found on line 21 +208: [16:05:51] WARNING: no name column found on line 22 +208: [16:05:51] WARNING: no name column found on line 23 +208: [16:05:51] WARNING: no name column found on line 24 +208: [16:05:51] WARNING: no name column found on line 25 +208: [16:05:51] WARNING: no name column found on line 26 +208: [16:05:51] WARNING: no name column found on line 27 +208: [16:05:51] WARNING: no name column found on line 28 +208: [16:05:51] WARNING: no name column found on line 29 +208: [16:05:51] WARNING: no name column found on line 30 +208: [16:05:51] WARNING: no name column found on line 31 +208: [16:05:51] WARNING: no name column found on line 32 +208: [16:05:51] WARNING: no name column found on line 33 +208: [16:05:51] WARNING: no name column found on line 34 +208: [16:05:51] WARNING: no name column found on line 35 +208: [16:05:51] WARNING: no name column found on line 36 +208: [16:05:51] WARNING: no name column found on line 37 +208: [16:05:51] WARNING: no name column found on line 38 +208: [16:05:51] WARNING: no name column found on line 39 +208: [16:05:51] WARNING: no name column found on line 40 +208: [16:05:51] WARNING: no name column found on line 41 +208: [16:05:51] WARNING: no name column found on line 42 +208: [16:05:51] WARNING: no name column found on line 43 +208: [16:05:51] WARNING: no name column found on line 44 +208: [16:05:51] WARNING: no name column found on line 45 +208: [16:05:51] WARNING: no name column found on line 46 +208: [16:05:51] WARNING: no name column found on line 47 +208: [16:05:51] WARNING: no name column found on line 48 +208: [16:05:51] WARNING: no name column found on line 49 +208: [16:05:51] WARNING: no name column found on line 50 +208: [16:05:51] WARNING: no name column found on line 51 +208: [16:05:51] WARNING: no name column found on line 52 +208: [16:05:51] WARNING: no name column found on line 53 +208: [16:05:51] WARNING: no name column found on line 54 +208: [16:05:51] WARNING: no name column found on line 55 +208: [16:05:51] WARNING: no name column found on line 56 +208: [16:05:51] WARNING: no name column found on line 57 +208: [16:05:51] WARNING: no name column found on line 58 +208: [16:05:51] WARNING: no name column found on line 59 +208: [16:05:51] WARNING: no name column found on line 60 +208: [16:05:51] WARNING: no name column found on line 61 +208: [16:05:51] WARNING: no name column found on line 62 +208: [16:05:51] WARNING: no name column found on line 63 +208: [16:05:51] WARNING: no name column found on line 64 +208: [16:05:51] WARNING: no name column found on line 65 +208: [16:05:51] WARNING: no name column found on line 66 +208: [16:05:51] WARNING: no name column found on line 67 +208: [16:05:51] WARNING: no name column found on line 68 +208: [16:05:51] WARNING: no name column found on line 69 +208: [16:05:51] WARNING: no name column found on line 70 +208: [16:05:51] WARNING: no name column found on line 71 +208: [16:05:51] WARNING: no name column found on line 72 +208: [16:05:51] WARNING: no name column found on line 73 +208: [16:05:51] WARNING: no name column found on line 74 +208: [16:05:51] WARNING: no name column found on line 75 +208: [16:05:51] WARNING: no name column found on line 76 +208: [16:05:51] WARNING: no name column found on line 77 +208: [16:05:51] WARNING: no name column found on line 78 +208: [16:05:51] WARNING: no name column found on line 79 +208: [16:05:51] WARNING: no name column found on line 80 +208: [16:05:51] WARNING: no name column found on line 81 +208: [16:05:51] WARNING: no name column found on line 82 +208: [16:05:51] WARNING: no name column found on line 83 +208: [16:05:51] WARNING: no name column found on line 84 +208: [16:05:51] WARNING: no name column found on line 85 +208: [16:05:51] WARNING: no name column found on line 86 +208: [16:05:51] WARNING: no name column found on line 87 +208: [16:05:51] WARNING: no name column found on line 88 +208: [16:05:51] WARNING: no name column found on line 89 +208: [16:05:51] WARNING: no name column found on line 90 +208: [16:05:51] WARNING: no name column found on line 91 +208: [16:05:51] WARNING: no name column found on line 92 +208: [16:05:51] WARNING: no name column found on line 93 +208: [16:05:51] WARNING: no name column found on line 94 +208: [16:05:51] WARNING: no name column found on line 95 +208: [16:05:51] WARNING: no name column found on line 96 +208: [16:05:51] WARNING: no name column found on line 97 +208: [16:05:51] WARNING: no name column found on line 98 +208: [16:05:51] WARNING: no name column found on line 99 +208: [16:05:51] WARNING: no name column found on line 100 +208: [16:05:51] WARNING: no name column found on line 101 +208: [16:05:51] WARNING: no name column found on line 102 +208: [16:05:51] WARNING: no name column found on line 103 +208: [16:05:51] WARNING: no name column found on line 104 +208: [16:05:51] WARNING: no name column found on line 105 +208: [16:05:51] WARNING: no name column found on line 106 +208: [16:05:51] WARNING: no name column found on line 107 +208: [16:05:51] WARNING: no name column found on line 108 +208: [16:05:51] WARNING: no name column found on line 109 +208: [16:05:51] WARNING: no name column found on line 110 +208: [16:05:51] WARNING: no name column found on line 111 +208: [16:05:51] WARNING: no name column found on line 112 +208: [16:05:51] WARNING: no name column found on line 113 +208: [16:05:51] WARNING: no name column found on line 114 +208: [16:05:51] WARNING: no name column found on line 115 +208: [16:05:51] WARNING: no name column found on line 116 +208: [16:05:51] WARNING: no name column found on line 117 +208: [16:05:51] WARNING: no name column found on line 118 +208: [16:05:51] WARNING: no name column found on line 119 +208: [16:05:51] WARNING: no name column found on line 120 +208: [16:05:51] WARNING: no name column found on line 121 +208: [16:05:51] WARNING: no name column found on line 122 +208: [16:05:51] WARNING: no name column found on line 123 +208: [16:05:51] WARNING: no name column found on line 124 +208: [16:05:51] WARNING: no name column found on line 125 +208: [16:05:51] WARNING: no name column found on line 126 +208: [16:05:51] WARNING: no name column found on line 127 +208: [16:05:51] WARNING: no name column found on line 128 +208: [16:05:51] WARNING: no name column found on line 129 +208: [16:05:51] WARNING: no name column found on line 130 +208: [16:05:51] WARNING: no name column found on line 131 +208: [16:05:51] WARNING: no name column found on line 132 +208: [16:05:51] WARNING: no name column found on line 133 +208: [16:05:51] WARNING: no name column found on line 134 +208: [16:05:51] WARNING: no name column found on line 135 +208: [16:05:51] WARNING: no name column found on line 136 +208: [16:05:51] WARNING: no name column found on line 137 +208: [16:05:51] WARNING: no name column found on line 138 +208: [16:05:51] WARNING: no name column found on line 139 +208: [16:05:51] WARNING: no name column found on line 140 +208: [16:05:51] WARNING: no name column found on line 141 +208: [16:05:51] WARNING: no name column found on line 142 +208: [16:05:51] WARNING: no name column found on line 143 +208: [16:05:51] WARNING: no name column found on line 144 +208: [16:05:51] WARNING: no name column found on line 145 +208: [16:05:51] WARNING: no name column found on line 146 +208: [16:05:51] WARNING: no name column found on line 147 +208: [16:05:51] WARNING: no name column found on line 148 +208: [16:05:51] WARNING: no name column found on line 149 +208: [16:05:51] WARNING: no name column found on line 150 +208: [16:05:51] WARNING: no name column found on line 151 +208: [16:05:51] WARNING: no name column found on line 152 +208: [16:05:51] WARNING: no name column found on line 153 +208: [16:05:51] WARNING: no name column found on line 154 +208: [16:05:51] WARNING: no name column found on line 155 +208: [16:05:51] WARNING: no name column found on line 156 +208: [16:05:51] WARNING: no name column found on line 157 +208: [16:05:51] WARNING: no name column found on line 158 +208: [16:05:51] WARNING: no name column found on line 159 +208: [16:05:51] WARNING: no name column found on line 160 +208: [16:05:51] WARNING: no name column found on line 161 +208: [16:05:51] WARNING: no name column found on line 162 +208: [16:05:51] WARNING: no name column found on line 163 +208: [16:05:51] WARNING: no name column found on line 164 +208: [16:05:51] WARNING: no name column found on line 165 +208: [16:05:51] WARNING: no name column found on line 166 +208: [16:05:51] WARNING: no name column found on line 167 +208: [16:05:51] WARNING: no name column found on line 168 +208: [16:05:51] WARNING: no name column found on line 169 +208: [16:05:51] WARNING: no name column found on line 170 +208: [16:05:51] WARNING: no name column found on line 171 +208: [16:05:51] WARNING: no name column found on line 172 +208: [16:05:51] WARNING: no name column found on line 173 +208: [16:05:51] WARNING: no name column found on line 174 +208: [16:05:51] WARNING: no name column found on line 175 +208: [16:05:51] WARNING: no name column found on line 176 +208: [16:05:51] WARNING: no name column found on line 177 +208: [16:05:51] WARNING: no name column found on line 178 +208: [16:05:51] WARNING: no name column found on line 179 +208: [16:05:51] WARNING: no name column found on line 180 +208: [16:05:51] WARNING: no name column found on line 181 +208: [16:05:51] WARNING: no name column found on line 182 +208: [16:05:51] WARNING: no name column found on line 183 +208: [16:05:51] WARNING: no name column found on line 184 +208: [16:05:51] WARNING: no name column found on line 185 +208: [16:05:51] WARNING: no name column found on line 186 +208: [16:05:51] WARNING: no name column found on line 187 +208: [16:05:51] WARNING: no name column found on line 188 +208: [16:05:51] WARNING: no name column found on line 189 +208: [16:05:51] WARNING: no name column found on line 190 +208: [16:05:51] WARNING: no name column found on line 191 +208: [16:05:51] WARNING: no name column found on line 192 +208: [16:05:51] WARNING: no name column found on line 193 +208: [16:05:51] WARNING: no name column found on line 194 +208: [16:05:51] WARNING: no name column found on line 195 +208: [16:05:51] WARNING: no name column found on line 196 +208: [16:05:51] WARNING: no name column found on line 197 +208: [16:05:51] WARNING: no name column found on line 198 +208: [16:05:51] WARNING: no name column found on line 199 +208: [16:05:51] WARNING: no name column found on line 200 +208: [16:05:51] WARNING: no name column found on line 201 +208: [16:05:51] WARNING: no name column found on line 202 +208: [16:05:51] WARNING: no name column found on line 203 +208: [16:05:51] WARNING: no name column found on line 204 +208: [16:05:51] WARNING: no name column found on line 205 +208: [16:05:51] WARNING: no name column found on line 206 +208: [16:05:51] WARNING: no name column found on line 207 +208: [16:05:51] WARNING: no name column found on line 208 +208: [16:05:51] WARNING: no name column found on line 209 +208: [16:05:51] WARNING: no name column found on line 210 +208: [16:05:51] WARNING: no name column found on line 211 +208: [16:05:51] WARNING: no name column found on line 212 +208: [16:05:51] WARNING: no name column found on line 213 +208: [16:05:51] WARNING: no name column found on line 214 +208: [16:05:51] WARNING: no name column found on line 215 +208: [16:05:51] WARNING: no name column found on line 216 208: ...... 208: ---------------------------------------------------------------------- -208: Ran 10 tests in 0.109s +208: Ran 10 tests in 0.138s 208: 208: OK -123: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 -123: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O 208: .................. 208: ---------------------------------------------------------------------- -208: Ran 18 tests in 0.604s +208: Ran 18 tests in 0.842s 208: 208: OK 208: ... 208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.080s +208: Ran 3 tests in 0.130s 208: 208: OK -123: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O 208: ........ 208: ---------------------------------------------------------------------- -208: Ran 8 tests in 0.023s +208: Ran 8 tests in 0.035s 208: 208: OK 208: .. 208: ---------------------------------------------------------------------- -208: Ran 2 tests in 0.016s +208: Ran 2 tests in 0.024s 208: 208: OK 208: .. 208: ---------------------------------------------------------------------- -208: Ran 2 tests in 0.012s +208: Ran 2 tests in 0.025s 208: 208: OK 208: . 208: ---------------------------------------------------------------------- -208: Ran 1 test in 0.069s +208: Ran 1 test in 0.099s 208: 208: OK -123: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O 208: ........ 208: ---------------------------------------------------------------------- -208: Ran 8 tests in 0.001s +208: Ran 8 tests in 0.002s 208: 208: OK 208: ... 208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.003s +208: Ran 3 tests in 0.004s 208: 208: OK 208: ... 208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.001s +208: Ran 3 tests in 0.002s 208: 208: OK 208: ...E @@ -32123,33 +32231,32 @@ 208: RuntimeError: Incomplete pickle support (__getstate_manages_dict__ not set) 208: 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.004s +208: Ran 4 tests in 0.006s 208: 208: FAILED (errors=1) 208: !!! TEST FAILURE: python UnitTestFeatMapUtils.py {} 208: ....... 208: ---------------------------------------------------------------------- -208: Ran 7 tests in 0.012s +208: Ran 7 tests in 0.019s 208: 208: OK -123: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 208: .... 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.014s +208: Ran 4 tests in 0.020s 208: 208: OK -123: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 -123: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 208: .... 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 1.979s +208: Ran 4 tests in 3.636s 208: 208: OK 208: .......... 208: ---------------------------------------------------------------------- -208: Ran 10 tests in 0.036s +208: Ran 10 tests in 0.057s 208: 208: OK +123: [16:06:01] Molecule does not have explicit Hs. Consider calling AddHs() +207/208 Test #123: testDistGeomHelpers .................... Passed 162.65 sec 208: . 208: ---------------------------------------------------------------------- 208: Ran 1 test in 0.000s @@ -32157,10 +32264,9 @@ 208: OK 208: .......... 208: ---------------------------------------------------------------------- -208: Ran 10 tests in 0.003s +208: Ran 10 tests in 0.004s 208: 208: OK -123: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 208: ....E 208: ====================================================================== 208: ERROR: testOrderBug2 (__main__.TestCase.testOrderBug2) @@ -32177,21 +32283,15 @@ 208: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 208: 208: ---------------------------------------------------------------------- -208: Ran 5 tests in 0.026s +208: Ran 5 tests in 0.051s 208: 208: FAILED (errors=1) 208: !!! TEST FAILURE: python UnitTestGobbi.py {} -123: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 -123: CC(=O)OC1=C(Sc2ccccc2)C[C@H]2Cc3cc4cccc(O)c4c(O)c3C(=O)[C@H]2C1 -123: Nc1ncnc2c1ncn2[C@@H]1C[C@H](CO)[C@@H](O)C1 -123: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 -123: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 -123: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] -208: ................[19:38:32] Molecule does not have explicit Hs. Consider calling AddHs() -208: [19:38:32] Molecule does not have explicit Hs. Consider calling AddHs() +208: ................[16:06:10] Molecule does not have explicit Hs. Consider calling AddHs() +208: [16:06:10] Molecule does not have explicit Hs. Consider calling AddHs() 208: ..... 208: ---------------------------------------------------------------------- -208: Ran 21 tests in 4.734s +208: Ran 21 tests in 8.478s 208: 208: OK 208: mol_197 @@ -32205,7 +32305,7 @@ 208: Ran 1 test in 0.000s 208: 208: OK -208: ...[19:38:33] +208: ...[16:06:11] 208: 208: **** 208: Pre-condition Violation @@ -32216,67 +32316,65 @@ 208: 208: . 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.016s +208: Ran 4 tests in 0.026s 208: 208: OK -123: [19:38:38] Molecule does not have explicit Hs. Consider calling AddHs() -207/208 Test #123: testDistGeomHelpers .................... Passed 88.03 sec 208: .. 208: ---------------------------------------------------------------------- -208: Ran 2 tests in 10.242s +208: Ran 2 tests in 17.217s 208: 208: OK 208: .. 208: ---------------------------------------------------------------------- -208: Ran 2 tests in 0.085s +208: Ran 2 tests in 0.118s 208: 208: OK 208: ... 208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.010s +208: Ran 3 tests in 0.015s 208: 208: OK 208: .... 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.017s +208: Ran 4 tests in 0.023s 208: 208: OK -208: .....[19:38:44] WARNING: not removing hydrogen atom without neighbors -208: [19:38:44] WARNING: not removing hydrogen atom without neighbors -208: [19:38:44] WARNING: not removing hydrogen atom without neighbors -208: [19:38:44] WARNING: not removing hydrogen atom without neighbors -208: [19:38:44] WARNING: not removing hydrogen atom without neighbors -208: [19:38:44] WARNING: not removing hydrogen atom without neighbors -208: [19:38:44] WARNING: not removing hydrogen atom without neighbors -208: [19:38:44] WARNING: not removing hydrogen atom without neighbors -208: [19:38:44] WARNING: not removing hydrogen atom without neighbors -208: [19:38:44] WARNING: not removing hydrogen atom without neighbors -208: [19:38:44] WARNING: not removing hydrogen atom without neighbors -208: [19:38:44] WARNING: not removing hydrogen atom without neighbors -208: [19:38:44] WARNING: not removing hydrogen atom without neighbors -208: [19:38:44] WARNING: not removing hydrogen atom without neighbors -208: [19:38:44] WARNING: not removing hydrogen atom without neighbors -208: [19:38:44] WARNING: not removing hydrogen atom without neighbors -208: [19:38:44] WARNING: not removing hydrogen atom without neighbors -208: [19:38:44] WARNING: not removing hydrogen atom without neighbors -208: [19:38:44] WARNING: not removing hydrogen atom without neighbors +208: .....[16:06:30] WARNING: not removing hydrogen atom without neighbors +208: [16:06:30] WARNING: not removing hydrogen atom without neighbors +208: [16:06:30] WARNING: not removing hydrogen atom without neighbors +208: [16:06:30] WARNING: not removing hydrogen atom without neighbors +208: [16:06:30] WARNING: not removing hydrogen atom without neighbors +208: [16:06:30] WARNING: not removing hydrogen atom without neighbors +208: [16:06:30] WARNING: not removing hydrogen atom without neighbors +208: [16:06:30] WARNING: not removing hydrogen atom without neighbors +208: [16:06:30] WARNING: not removing hydrogen atom without neighbors +208: [16:06:30] WARNING: not removing hydrogen atom without neighbors +208: [16:06:30] WARNING: not removing hydrogen atom without neighbors +208: [16:06:30] WARNING: not removing hydrogen atom without neighbors +208: [16:06:30] WARNING: not removing hydrogen atom without neighbors +208: [16:06:30] WARNING: not removing hydrogen atom without neighbors +208: [16:06:30] WARNING: not removing hydrogen atom without neighbors +208: [16:06:30] WARNING: not removing hydrogen atom without neighbors +208: [16:06:30] WARNING: not removing hydrogen atom without neighbors +208: [16:06:30] WARNING: not removing hydrogen atom without neighbors +208: [16:06:30] WARNING: not removing hydrogen atom without neighbors 208: ..... 208: ---------------------------------------------------------------------- -208: Ran 10 tests in 0.316s +208: Ran 10 tests in 0.491s 208: 208: OK -208: ssssss[19:38:45] No suitable metadata found. -208: .[19:38:45] No suitable metadata found. +208: ssssss[16:06:31] No suitable metadata found. +208: .[16:06:31] No suitable metadata found. 208: ......s/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/Draw/__init__.py:237: DeprecationWarning: legacy DrawingOptions not translated for new drawing code, please update manually 208: warnings.warn( 208: ..... 208: ---------------------------------------------------------------------- -208: Ran 19 tests in 0.323s +208: Ran 19 tests in 0.486s 208: 208: OK (skipped=7) 208: sss. 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.654s +208: Ran 4 tests in 1.014s 208: 208: OK (skipped=3) 208: sss @@ -32286,33 +32384,33 @@ 208: OK (skipped=3) 208: .......... 208: ---------------------------------------------------------------------- -208: Ran 10 tests in 0.537s +208: Ran 10 tests in 0.931s 208: 208: OK -208: ..[19:38:47] SMARTS Parse Error: syntax error while parsing: boromicacid -208: [19:38:47] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -208: [19:38:47] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -208: [19:38:47] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -208: [19:38:47] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -208: [19:38:47] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -208: [19:38:47] reaction has no reactants -208: [19:38:47] reaction has no products -208: [19:38:47] initialization failed -208: [19:38:47] reaction has no reactants -208: [19:38:47] reaction has no products +208: ..[16:06:34] SMARTS Parse Error: syntax error while parsing: boromicacid +208: [16:06:34] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +208: [16:06:34] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +208: [16:06:34] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +208: [16:06:34] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +208: [16:06:34] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +208: [16:06:34] reaction has no reactants +208: [16:06:34] reaction has no products +208: [16:06:34] initialization failed +208: [16:06:34] reaction has no reactants +208: [16:06:34] reaction has no products 208: . 208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.021s +208: Ran 3 tests in 0.029s 208: 208: OK 208: .... 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.010s +208: Ran 4 tests in 0.014s 208: 208: OK 208: .................... 208: ---------------------------------------------------------------------- -208: Ran 20 tests in 0.109s +208: Ran 20 tests in 0.144s 208: 208: OK 208: !!! TEST FAILURE: python UnitTestGraphDescriptors_2.py {} @@ -32322,18 +32420,18 @@ 208: !!! TEST FAILURE: python UnitTestDocTestsChem.py {} 208: !!! TEST FAILURE: python test_list.py {'dir': 'FeatMaps'} 208: !!! TEST FAILURE: python test_list.py {'dir': 'Pharm2D'} -208/208 Test #208: pythonTestDirChem ......................***Failed 80.66 sec +208/208 Test #208: pythonTestDirChem ......................***Failed 138.81 sec ....... ---------------------------------------------------------------------- -Ran 7 tests in 0.135s +Ran 7 tests in 0.147s OK ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.055s +Ran 6 tests in 0.059s OK -....[19:37:28] +....[16:04:18] **** Pre-condition Violation @@ -32344,22 +32442,22 @@ . ---------------------------------------------------------------------- -Ran 5 tests in 0.008s +Ran 5 tests in 0.017s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.011s +Ran 4 tests in 0.012s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.014s +Ran 2 tests in 0.012s OK ...................... ---------------------------------------------------------------------- -Ran 22 tests in 0.032s +Ran 22 tests in 0.039s OK .....s..........E......ss @@ -32384,51 +32482,51 @@ https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations ---------------------------------------------------------------------- -Ran 25 tests in 0.165s +Ran 25 tests in 0.180s FAILED (errors=1, skipped=3) ..s ---------------------------------------------------------------------- -Ran 3 tests in 0.191s +Ran 3 tests in 0.219s OK (skipped=1) ................................... ---------------------------------------------------------------------- -Ran 35 tests in 1.056s +Ran 35 tests in 1.058s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.025s +Ran 4 tests in 0.028s OK . ---------------------------------------------------------------------- -Ran 1 test in 0.016s +Ran 1 test in 0.018s OK ....... ---------------------------------------------------------------------- -Ran 7 tests in 0.040s +Ran 7 tests in 0.064s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.046s +Ran 3 tests in 0.060s OK .ss.ss....... ---------------------------------------------------------------------- -Ran 13 tests in 1.147s +Ran 13 tests in 1.856s OK (skipped=4) -[19:37:34] Molecule does not have explicit Hs. Consider calling AddHs() -.[19:37:34] Molecule does not have explicit Hs. Consider calling AddHs() -.........F........[19:38:01] WARNING: More than one matching pattern found - picking one +[16:04:25] Molecule does not have explicit Hs. Consider calling AddHs() +.[16:04:25] Molecule does not have explicit Hs. Consider calling AddHs() +.........F........[16:05:20] WARNING: More than one matching pattern found - picking one -[19:38:01] WARNING: More than one matching pattern found - picking one +[16:05:20] WARNING: More than one matching pattern found - picking one -.[19:38:01] WARNING: More than one matching pattern found - picking one +.[16:05:20] WARNING: More than one matching pattern found - picking one ... ====================================================================== @@ -32438,19 +32536,19 @@ File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/UnitTestMol3D.py", line 244, in testEnumerateStereoisomersRandomSamplingShouldBeDeterministicAndPortable self.assertEqual(smiles, expected) AssertionError: Items in the first set but not the second: -'C/C(F)=C/[C@@H](Cl)/C=C(\\Br)[C@@H](N)I' 'C/C(F)=C/[C@@H](Cl)/C=C(/Br)[C@@H](N)I' +'C/C(F)=C/[C@@H](Cl)/C=C(\\Br)[C@@H](N)I' Items in the second set but not the first: 'C/C(F)=C/[C@@H](Cl)/C=C(\\Br)[C@H](N)I' 'C/C(F)=C\\[C@H](Cl)/C=C(\\Br)[C@H](N)I' ---------------------------------------------------------------------- -Ran 23 tests in 29.691s +Ran 23 tests in 58.579s FAILED (failures=1) -{'C/C(F)=C\\[C@@H](C)Cl', 'C/C(F)=C/[C@@H](C)Cl', 'C/C(F)=C\\[C@H](C)Cl', 'C/C(F)=C/[C@H](C)Cl'} -{'C/C(F)=C\\[C@@H](C)Cl', 'C/C(F)=C/[C@@H](C)Cl', 'C/C(F)=C\\[C@H](C)Cl', 'C/C(F)=C/[C@H](C)Cl'} -{'F[C@H](Cl)[C@@H](F)Cl', 'F[C@@H](Cl)[C@@H](F)Cl', 'F[C@H](Cl)[C@H](F)Cl'} +{'C/C(F)=C\\[C@H](C)Cl', 'C/C(F)=C/[C@H](C)Cl', 'C/C(F)=C\\[C@@H](C)Cl', 'C/C(F)=C/[C@@H](C)Cl'} +{'C/C(F)=C\\[C@H](C)Cl', 'C/C(F)=C/[C@H](C)Cl', 'C/C(F)=C\\[C@@H](C)Cl', 'C/C(F)=C/[C@@H](C)Cl'} +{'F[C@H](Cl)[C@H](F)Cl', 'F[C@@H](Cl)[C@@H](F)Cl', 'F[C@H](Cl)[C@@H](F)Cl'} .....E.. ====================================================================== ERROR: test7ScoreMolecules (__main__.TestCase.test7ScoreMolecules) @@ -32470,7 +32568,7 @@ https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations ---------------------------------------------------------------------- -Ran 8 tests in 0.088s +Ran 8 tests in 0.118s FAILED (errors=1) Traceback (most recent call last): @@ -32505,10 +32603,10 @@ `np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here. The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations -F..[19:38:07] WARNING: not removing hydrogen atom without neighbors -[19:38:07] WARNING: not removing hydrogen atom without neighbors -[19:38:07] WARNING: not removing hydrogen atom without neighbors -....[19:38:07] WARNING: not removing hydrogen atom without neighbors +F..[16:05:28] WARNING: not removing hydrogen atom without neighbors +[16:05:28] WARNING: not removing hydrogen atom without neighbors +[16:05:28] WARNING: not removing hydrogen atom without neighbors +....[16:05:28] WARNING: not removing hydrogen atom without neighbors ...... ====================================================================== FAIL: testBadAtomHandling (__main__.TestCase.testBadAtomHandling) @@ -32565,17 +32663,17 @@ AssertionError: SMILES: CCC; Descriptor: Ipc ---------------------------------------------------------------------- -Ran 14 tests in 2.553s +Ran 14 tests in 3.598s FAILED (failures=2) .... ---------------------------------------------------------------------- -Ran 4 tests in 1.019s +Ran 4 tests in 1.500s OK ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.269s +Ran 6 tests in 0.341s OK .......:1: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. @@ -32586,17 +32684,17 @@ antibiotics = antibiotics.append({ .......s..s........ ---------------------------------------------------------------------- -Ran 26 tests in 1.701s +Ran 26 tests in 2.593s OK (skipped=2) -.............F[19:38:19] WARNING: More than one matching pattern found - picking one +.............F[16:05:49] WARNING: More than one matching pattern found - picking one -[19:38:19] WARNING: More than one matching pattern found - picking one +[16:05:49] WARNING: More than one matching pattern found - picking one -..[19:38:19] Molecule does not have explicit Hs. Consider calling AddHs() -[19:38:19] Molecule does not have explicit Hs. Consider calling AddHs() -[19:38:19] Molecule does not have explicit Hs. Consider calling AddHs() -[19:38:19] Molecule does not have explicit Hs. Consider calling AddHs() +..[16:05:49] Molecule does not have explicit Hs. Consider calling AddHs() +[16:05:49] Molecule does not have explicit Hs. Consider calling AddHs() +[16:05:49] Molecule does not have explicit Hs. Consider calling AddHs() +[16:05:49] Molecule does not have explicit Hs. Consider calling AddHs() ......... ====================================================================== FAIL: FindBRICSBonds (rdkit.Chem.BRICS) @@ -32625,285 +32723,285 @@ ---------------------------------------------------------------------- -Ran 25 tests in 7.872s +Ran 25 tests in 14.241s FAILED (failures=1) .. ---------------------------------------------------------------------- -Ran 2 tests in 0.040s +Ran 2 tests in 0.056s OK ..s... ---------------------------------------------------------------------- -Ran 6 tests in 0.627s +Ran 6 tests in 0.904s OK (skipped=1) -..[19:38:21] WARNING: not removing hydrogen atom without neighbors -.[19:38:21] WARNING: not removing hydrogen atom without neighbors -.[19:38:21] WARNING: no name column found on line 1 -[19:38:21] WARNING: no name column found on line 2 -[19:38:21] WARNING: no name column found on line 3 -[19:38:21] WARNING: no name column found on line 4 -[19:38:21] WARNING: no name column found on line 5 -[19:38:21] WARNING: no name column found on line 6 -[19:38:21] WARNING: no name column found on line 7 -[19:38:21] WARNING: no name column found on line 8 -[19:38:21] WARNING: no name column found on line 9 -[19:38:21] WARNING: no name column found on line 10 -[19:38:21] WARNING: no name column found on line 11 -[19:38:21] WARNING: no name column found on line 12 -[19:38:21] WARNING: no name column found on line 13 -[19:38:21] WARNING: no name column found on line 14 -[19:38:21] WARNING: no name column found on line 15 -[19:38:21] WARNING: no name column found on line 16 -[19:38:21] WARNING: no name column found on line 17 -[19:38:21] WARNING: no name column found on line 18 -[19:38:21] WARNING: no name column found on line 19 -[19:38:21] WARNING: no name column found on line 20 -[19:38:21] WARNING: no name column found on line 21 -[19:38:21] WARNING: no name column found on line 22 -[19:38:21] WARNING: no name column found on line 23 -[19:38:21] WARNING: no name column found on line 24 -[19:38:21] WARNING: no name column found on line 25 -[19:38:21] WARNING: no name column found on line 26 -[19:38:21] WARNING: no name column found on line 27 -[19:38:21] WARNING: no name column found on line 28 -[19:38:21] WARNING: no name column found on line 29 -[19:38:21] WARNING: no name column found on line 30 -[19:38:21] WARNING: no name column found on line 31 -[19:38:21] WARNING: no name column found on line 32 -[19:38:21] WARNING: no name column found on line 33 -[19:38:21] WARNING: no name column found on line 34 -[19:38:21] WARNING: no name column found on line 35 -[19:38:21] WARNING: no name column found on line 36 -[19:38:21] WARNING: no name column found on line 37 -[19:38:21] WARNING: no name column found on line 38 -[19:38:21] WARNING: no name column found on line 39 -[19:38:21] WARNING: no name column found on line 40 -[19:38:21] WARNING: no name column found on line 41 -[19:38:21] WARNING: no name column found on line 42 -[19:38:21] WARNING: no name column found on line 43 -[19:38:21] WARNING: no name column found on line 44 -[19:38:21] WARNING: no name column found on line 45 -[19:38:21] WARNING: no name column found on line 46 -[19:38:21] WARNING: no name column found on line 47 -[19:38:21] WARNING: no name column found on line 48 -[19:38:21] WARNING: no name column found on line 49 -[19:38:21] WARNING: no name column found on line 50 -[19:38:21] WARNING: no name column found on line 51 -[19:38:21] WARNING: no name column found on line 52 -[19:38:21] WARNING: no name column found on line 53 -[19:38:21] WARNING: no name column found on line 54 -[19:38:21] WARNING: no name column found on line 55 -[19:38:21] WARNING: no name column found on line 56 -[19:38:21] WARNING: no name column found on line 57 -[19:38:21] WARNING: no name column found on line 58 -[19:38:21] WARNING: no name column found on line 59 -[19:38:21] WARNING: no name column found on line 60 -[19:38:21] WARNING: no name column found on line 61 -[19:38:21] WARNING: no name column found on line 62 -[19:38:21] WARNING: no name column found on line 63 -[19:38:21] WARNING: no name column found on line 64 -[19:38:21] WARNING: no name column found on line 65 -[19:38:21] WARNING: no name column found on line 66 -[19:38:21] WARNING: no name column found on line 67 -[19:38:21] WARNING: no name column found on line 68 -[19:38:21] WARNING: no name column found on line 69 -[19:38:21] WARNING: no name column found on line 70 -[19:38:21] WARNING: no name column found on line 71 -[19:38:21] WARNING: no name column found on line 72 -[19:38:21] WARNING: no name column found on line 73 -[19:38:21] WARNING: no name column found on line 74 -[19:38:21] WARNING: no name column found on line 75 -[19:38:21] WARNING: no name column found on line 76 -[19:38:21] WARNING: no name column found on line 77 -[19:38:21] WARNING: no name column found on line 78 -[19:38:21] WARNING: no name column found on line 79 -[19:38:21] WARNING: no name column found on line 80 -[19:38:21] WARNING: no name column found on line 81 -[19:38:21] WARNING: no name column found on line 82 -[19:38:21] WARNING: no name column found on line 83 -[19:38:21] WARNING: no name column found on line 84 -[19:38:21] WARNING: no name column found on line 85 -[19:38:21] WARNING: no name column found on line 86 -[19:38:21] WARNING: no name column found on line 87 -[19:38:21] WARNING: no name column found on line 88 -[19:38:21] WARNING: no name column found on line 89 -[19:38:21] WARNING: no name column found on line 90 -[19:38:21] WARNING: no name column found on line 91 -[19:38:21] WARNING: no name column found on line 92 -[19:38:21] WARNING: no name column found on line 93 -[19:38:21] WARNING: no name column found on line 94 -[19:38:21] WARNING: no name column found on line 95 -[19:38:21] WARNING: no name column found on line 96 -[19:38:21] WARNING: no name column found on line 97 -[19:38:21] WARNING: no name column found on line 98 -[19:38:21] WARNING: no name column found on line 99 -[19:38:21] WARNING: no name column found on line 100 -[19:38:21] WARNING: no name column found on line 101 -[19:38:21] WARNING: no name column found on line 102 -[19:38:21] WARNING: no name column found on line 103 -[19:38:21] WARNING: no name column found on line 104 -[19:38:21] WARNING: no name column found on line 105 -[19:38:21] WARNING: no name column found on line 106 -[19:38:21] WARNING: no name column found on line 107 -[19:38:21] WARNING: no name column found on line 108 -[19:38:21] WARNING: no name column found on line 109 -[19:38:21] WARNING: no name column found on line 110 -[19:38:21] WARNING: no name column found on line 111 -[19:38:21] WARNING: no name column found on line 112 -[19:38:21] WARNING: no name column found on line 113 -[19:38:21] WARNING: no name column found on line 114 -[19:38:21] WARNING: no name column found on line 115 -[19:38:21] WARNING: no name column found on line 116 -[19:38:21] WARNING: no name column found on line 117 -[19:38:21] WARNING: no name column found on line 118 -[19:38:21] WARNING: no name column found on line 119 -[19:38:21] WARNING: no name column found on line 120 -[19:38:21] WARNING: no name column found on line 121 -[19:38:21] WARNING: no name column found on line 122 -[19:38:21] WARNING: no name column found on line 123 -[19:38:21] WARNING: no name column found on line 124 -[19:38:21] WARNING: no name column found on line 125 -[19:38:21] WARNING: no name column found on line 126 -[19:38:21] WARNING: no name column found on line 127 -[19:38:21] WARNING: no name column found on line 128 -[19:38:21] WARNING: no name column found on line 129 -[19:38:21] WARNING: no name column found on line 130 -[19:38:21] WARNING: no name column found on line 131 -[19:38:21] WARNING: no name column found on line 132 -[19:38:21] WARNING: no name column found on line 133 -[19:38:21] WARNING: no name column found on line 134 -[19:38:21] WARNING: no name column found on line 135 -[19:38:21] WARNING: no name column found on line 136 -[19:38:21] WARNING: no name column found on line 137 -[19:38:21] WARNING: no name column found on line 138 -[19:38:21] WARNING: no name column found on line 139 -[19:38:21] WARNING: no name column found on line 140 -[19:38:21] WARNING: no name column found on line 141 -[19:38:21] WARNING: no name column found on line 142 -[19:38:21] WARNING: no name column found on line 143 -[19:38:21] WARNING: no name column found on line 144 -[19:38:21] WARNING: no name column found on line 145 -[19:38:21] WARNING: no name column found on line 146 -[19:38:21] WARNING: no name column found on line 147 -[19:38:21] WARNING: no name column found on line 148 -[19:38:21] WARNING: no name column found on line 149 -[19:38:21] WARNING: no name column found on line 150 -[19:38:21] WARNING: no name column found on line 151 -[19:38:21] WARNING: no name column found on line 152 -[19:38:21] WARNING: no name column found on line 153 -[19:38:21] WARNING: no name column found on line 154 -[19:38:21] WARNING: no name column found on line 155 -[19:38:21] WARNING: no name column found on line 156 -[19:38:21] WARNING: no name column found on line 157 -[19:38:21] WARNING: no name column found on line 158 -[19:38:21] WARNING: no name column found on line 159 -[19:38:21] WARNING: no name column found on line 160 -[19:38:21] WARNING: no name column found on line 161 -[19:38:21] WARNING: no name column found on line 162 -[19:38:21] WARNING: no name column found on line 163 -[19:38:21] WARNING: no name column found on line 164 -[19:38:21] WARNING: no name column found on line 165 -[19:38:21] WARNING: no name column found on line 166 -[19:38:21] WARNING: no name column found on line 167 -[19:38:21] WARNING: no name column found on line 168 -[19:38:21] WARNING: no name column found on line 169 -[19:38:21] WARNING: no name column found on line 170 -[19:38:21] WARNING: no name column found on line 171 -[19:38:21] WARNING: no name column found on line 172 -[19:38:21] WARNING: no name column found on line 173 -[19:38:21] WARNING: no name column found on line 174 -[19:38:21] WARNING: no name column found on line 175 -[19:38:21] WARNING: no name column found on line 176 -[19:38:21] WARNING: no name column found on line 177 -[19:38:21] WARNING: no name column found on line 178 -[19:38:21] WARNING: no name column found on line 179 -[19:38:21] WARNING: no name column found on line 180 -[19:38:21] WARNING: no name column found on line 181 -[19:38:21] WARNING: no name column found on line 182 -[19:38:21] WARNING: no name column found on line 183 -[19:38:21] WARNING: no name column found on line 184 -[19:38:21] WARNING: no name column found on line 185 -[19:38:21] WARNING: no name column found on line 186 -[19:38:21] WARNING: no name column found on line 187 -[19:38:21] WARNING: no name column found on line 188 -[19:38:21] WARNING: no name column found on line 189 -[19:38:21] WARNING: no name column found on line 190 -[19:38:21] WARNING: no name column found on line 191 -[19:38:21] WARNING: no name column found on line 192 -[19:38:21] WARNING: no name column found on line 193 -[19:38:21] WARNING: no name column found on line 194 -[19:38:21] WARNING: no name column found on line 195 -[19:38:21] WARNING: no name column found on line 196 -[19:38:21] WARNING: no name column found on line 197 -[19:38:21] WARNING: no name column found on line 198 -[19:38:21] WARNING: no name column found on line 199 -[19:38:21] WARNING: no name column found on line 200 -[19:38:21] WARNING: no name column found on line 201 -[19:38:21] WARNING: no name column found on line 202 -[19:38:21] WARNING: no name column found on line 203 -[19:38:21] WARNING: no name column found on line 204 -[19:38:21] WARNING: no name column found on line 205 -[19:38:21] WARNING: no name column found on line 206 -[19:38:21] WARNING: no name column found on line 207 -[19:38:21] WARNING: no name column found on line 208 -[19:38:21] WARNING: no name column found on line 209 -[19:38:21] WARNING: no name column found on line 210 -[19:38:21] WARNING: no name column found on line 211 -[19:38:21] WARNING: no name column found on line 212 -[19:38:21] WARNING: no name column found on line 213 -[19:38:21] WARNING: no name column found on line 214 -[19:38:21] WARNING: no name column found on line 215 -[19:38:21] WARNING: no name column found on line 216 +..[16:05:51] WARNING: not removing hydrogen atom without neighbors +.[16:05:51] WARNING: not removing hydrogen atom without neighbors +.[16:05:51] WARNING: no name column found on line 1 +[16:05:51] WARNING: no name column found on line 2 +[16:05:51] WARNING: no name column found on line 3 +[16:05:51] WARNING: no name column found on line 4 +[16:05:51] WARNING: no name column found on line 5 +[16:05:51] WARNING: no name column found on line 6 +[16:05:51] WARNING: no name column found on line 7 +[16:05:51] WARNING: no name column found on line 8 +[16:05:51] WARNING: no name column found on line 9 +[16:05:51] WARNING: no name column found on line 10 +[16:05:51] WARNING: no name column found on line 11 +[16:05:51] WARNING: no name column found on line 12 +[16:05:51] WARNING: no name column found on line 13 +[16:05:51] WARNING: no name column found on line 14 +[16:05:51] WARNING: no name column found on line 15 +[16:05:51] WARNING: no name column found on line 16 +[16:05:51] WARNING: no name column found on line 17 +[16:05:51] WARNING: no name column found on line 18 +[16:05:51] WARNING: no name column found on line 19 +[16:05:51] WARNING: no name column found on line 20 +[16:05:51] WARNING: no name column found on line 21 +[16:05:51] WARNING: no name column found on line 22 +[16:05:51] WARNING: no name column found on line 23 +[16:05:51] WARNING: no name column found on line 24 +[16:05:51] WARNING: no name column found on line 25 +[16:05:51] WARNING: no name column found on line 26 +[16:05:51] WARNING: no name column found on line 27 +[16:05:51] WARNING: no name column found on line 28 +[16:05:51] WARNING: no name column found on line 29 +[16:05:51] WARNING: no name column found on line 30 +[16:05:51] WARNING: no name column found on line 31 +[16:05:51] WARNING: no name column found on line 32 +[16:05:51] WARNING: no name column found on line 33 +[16:05:51] WARNING: no name column found on line 34 +[16:05:51] WARNING: no name column found on line 35 +[16:05:51] WARNING: no name column found on line 36 +[16:05:51] WARNING: no name column found on line 37 +[16:05:51] WARNING: no name column found on line 38 +[16:05:51] WARNING: no name column found on line 39 +[16:05:51] WARNING: no name column found on line 40 +[16:05:51] WARNING: no name column found on line 41 +[16:05:51] WARNING: no name column found on line 42 +[16:05:51] WARNING: no name column found on line 43 +[16:05:51] WARNING: no name column found on line 44 +[16:05:51] WARNING: no name column found on line 45 +[16:05:51] WARNING: no name column found on line 46 +[16:05:51] WARNING: no name column found on line 47 +[16:05:51] WARNING: no name column found on line 48 +[16:05:51] WARNING: no name column found on line 49 +[16:05:51] WARNING: no name column found on line 50 +[16:05:51] WARNING: no name column found on line 51 +[16:05:51] WARNING: no name column found on line 52 +[16:05:51] WARNING: no name column found on line 53 +[16:05:51] WARNING: no name column found on line 54 +[16:05:51] WARNING: no name column found on line 55 +[16:05:51] WARNING: no name column found on line 56 +[16:05:51] WARNING: no name column found on line 57 +[16:05:51] WARNING: no name column found on line 58 +[16:05:51] WARNING: no name column found on line 59 +[16:05:51] WARNING: no name column found on line 60 +[16:05:51] WARNING: no name column found on line 61 +[16:05:51] WARNING: no name column found on line 62 +[16:05:51] WARNING: no name column found on line 63 +[16:05:51] WARNING: no name column found on line 64 +[16:05:51] WARNING: no name column found on line 65 +[16:05:51] WARNING: no name column found on line 66 +[16:05:51] WARNING: no name column found on line 67 +[16:05:51] WARNING: no name column found on line 68 +[16:05:51] WARNING: no name column found on line 69 +[16:05:51] WARNING: no name column found on line 70 +[16:05:51] WARNING: no name column found on line 71 +[16:05:51] WARNING: no name column found on line 72 +[16:05:51] WARNING: no name column found on line 73 +[16:05:51] WARNING: no name column found on line 74 +[16:05:51] WARNING: no name column found on line 75 +[16:05:51] WARNING: no name column found on line 76 +[16:05:51] WARNING: no name column found on line 77 +[16:05:51] WARNING: no name column found on line 78 +[16:05:51] WARNING: no name column found on line 79 +[16:05:51] WARNING: no name column found on line 80 +[16:05:51] WARNING: no name column found on line 81 +[16:05:51] WARNING: no name column found on line 82 +[16:05:51] WARNING: no name column found on line 83 +[16:05:51] WARNING: no name column found on line 84 +[16:05:51] WARNING: no name column found on line 85 +[16:05:51] WARNING: no name column found on line 86 +[16:05:51] WARNING: no name column found on line 87 +[16:05:51] WARNING: no name column found on line 88 +[16:05:51] WARNING: no name column found on line 89 +[16:05:51] WARNING: no name column found on line 90 +[16:05:51] WARNING: no name column found on line 91 +[16:05:51] WARNING: no name column found on line 92 +[16:05:51] WARNING: no name column found on line 93 +[16:05:51] WARNING: no name column found on line 94 +[16:05:51] WARNING: no name column found on line 95 +[16:05:51] WARNING: no name column found on line 96 +[16:05:51] WARNING: no name column found on line 97 +[16:05:51] WARNING: no name column found on line 98 +[16:05:51] WARNING: no name column found on line 99 +[16:05:51] WARNING: no name column found on line 100 +[16:05:51] WARNING: no name column found on line 101 +[16:05:51] WARNING: no name column found on line 102 +[16:05:51] WARNING: no name column found on line 103 +[16:05:51] WARNING: no name column found on line 104 +[16:05:51] WARNING: no name column found on line 105 +[16:05:51] WARNING: no name column found on line 106 +[16:05:51] WARNING: no name column found on line 107 +[16:05:51] WARNING: no name column found on line 108 +[16:05:51] WARNING: no name column found on line 109 +[16:05:51] WARNING: no name column found on line 110 +[16:05:51] WARNING: no name column found on line 111 +[16:05:51] WARNING: no name column found on line 112 +[16:05:51] WARNING: no name column found on line 113 +[16:05:51] WARNING: no name column found on line 114 +[16:05:51] WARNING: no name column found on line 115 +[16:05:51] WARNING: no name column found on line 116 +[16:05:51] WARNING: no name column found on line 117 +[16:05:51] WARNING: no name column found on line 118 +[16:05:51] WARNING: no name column found on line 119 +[16:05:51] WARNING: no name column found on line 120 +[16:05:51] WARNING: no name column found on line 121 +[16:05:51] WARNING: no name column found on line 122 +[16:05:51] WARNING: no name column found on line 123 +[16:05:51] WARNING: no name column found on line 124 +[16:05:51] WARNING: no name column found on line 125 +[16:05:51] WARNING: no name column found on line 126 +[16:05:51] WARNING: no name column found on line 127 +[16:05:51] WARNING: no name column found on line 128 +[16:05:51] WARNING: no name column found on line 129 +[16:05:51] WARNING: no name column found on line 130 +[16:05:51] WARNING: no name column found on line 131 +[16:05:51] WARNING: no name column found on line 132 +[16:05:51] WARNING: no name column found on line 133 +[16:05:51] WARNING: no name column found on line 134 +[16:05:51] WARNING: no name column found on line 135 +[16:05:51] WARNING: no name column found on line 136 +[16:05:51] WARNING: no name column found on line 137 +[16:05:51] WARNING: no name column found on line 138 +[16:05:51] WARNING: no name column found on line 139 +[16:05:51] WARNING: no name column found on line 140 +[16:05:51] WARNING: no name column found on line 141 +[16:05:51] WARNING: no name column found on line 142 +[16:05:51] WARNING: no name column found on line 143 +[16:05:51] WARNING: no name column found on line 144 +[16:05:51] WARNING: no name column found on line 145 +[16:05:51] WARNING: no name column found on line 146 +[16:05:51] WARNING: no name column found on line 147 +[16:05:51] WARNING: no name column found on line 148 +[16:05:51] WARNING: no name column found on line 149 +[16:05:51] WARNING: no name column found on line 150 +[16:05:51] WARNING: no name column found on line 151 +[16:05:51] WARNING: no name column found on line 152 +[16:05:51] WARNING: no name column found on line 153 +[16:05:51] WARNING: no name column found on line 154 +[16:05:51] WARNING: no name column found on line 155 +[16:05:51] WARNING: no name column found on line 156 +[16:05:51] WARNING: no name column found on line 157 +[16:05:51] WARNING: no name column found on line 158 +[16:05:51] WARNING: no name column found on line 159 +[16:05:51] WARNING: no name column found on line 160 +[16:05:51] WARNING: no name column found on line 161 +[16:05:51] WARNING: no name column found on line 162 +[16:05:51] WARNING: no name column found on line 163 +[16:05:51] WARNING: no name column found on line 164 +[16:05:51] WARNING: no name column found on line 165 +[16:05:51] WARNING: no name column found on line 166 +[16:05:51] WARNING: no name column found on line 167 +[16:05:51] WARNING: no name column found on line 168 +[16:05:51] WARNING: no name column found on line 169 +[16:05:51] WARNING: no name column found on line 170 +[16:05:51] WARNING: no name column found on line 171 +[16:05:51] WARNING: no name column found on line 172 +[16:05:51] WARNING: no name column found on line 173 +[16:05:51] WARNING: no name column found on line 174 +[16:05:51] WARNING: no name column found on line 175 +[16:05:51] WARNING: no name column found on line 176 +[16:05:51] WARNING: no name column found on line 177 +[16:05:51] WARNING: no name column found on line 178 +[16:05:51] WARNING: no name column found on line 179 +[16:05:51] WARNING: no name column found on line 180 +[16:05:51] WARNING: no name column found on line 181 +[16:05:51] WARNING: no name column found on line 182 +[16:05:51] WARNING: no name column found on line 183 +[16:05:51] WARNING: no name column found on line 184 +[16:05:51] WARNING: no name column found on line 185 +[16:05:51] WARNING: no name column found on line 186 +[16:05:51] WARNING: no name column found on line 187 +[16:05:51] WARNING: no name column found on line 188 +[16:05:51] WARNING: no name column found on line 189 +[16:05:51] WARNING: no name column found on line 190 +[16:05:51] WARNING: no name column found on line 191 +[16:05:51] WARNING: no name column found on line 192 +[16:05:51] WARNING: no name column found on line 193 +[16:05:51] WARNING: no name column found on line 194 +[16:05:51] WARNING: no name column found on line 195 +[16:05:51] WARNING: no name column found on line 196 +[16:05:51] WARNING: no name column found on line 197 +[16:05:51] WARNING: no name column found on line 198 +[16:05:51] WARNING: no name column found on line 199 +[16:05:51] WARNING: no name column found on line 200 +[16:05:51] WARNING: no name column found on line 201 +[16:05:51] WARNING: no name column found on line 202 +[16:05:51] WARNING: no name column found on line 203 +[16:05:51] WARNING: no name column found on line 204 +[16:05:51] WARNING: no name column found on line 205 +[16:05:51] WARNING: no name column found on line 206 +[16:05:51] WARNING: no name column found on line 207 +[16:05:51] WARNING: no name column found on line 208 +[16:05:51] WARNING: no name column found on line 209 +[16:05:51] WARNING: no name column found on line 210 +[16:05:51] WARNING: no name column found on line 211 +[16:05:51] WARNING: no name column found on line 212 +[16:05:51] WARNING: no name column found on line 213 +[16:05:51] WARNING: no name column found on line 214 +[16:05:51] WARNING: no name column found on line 215 +[16:05:51] WARNING: no name column found on line 216 ...... ---------------------------------------------------------------------- -Ran 10 tests in 0.109s +Ran 10 tests in 0.138s OK .................. ---------------------------------------------------------------------- -Ran 18 tests in 0.604s +Ran 18 tests in 0.842s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.080s +Ran 3 tests in 0.130s OK ........ ---------------------------------------------------------------------- -Ran 8 tests in 0.023s +Ran 8 tests in 0.035s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.016s +Ran 2 tests in 0.024s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.012s +Ran 2 tests in 0.025s OK . ---------------------------------------------------------------------- -Ran 1 test in 0.069s +Ran 1 test in 0.099s OK ........ ---------------------------------------------------------------------- -Ran 8 tests in 0.001s +Ran 8 tests in 0.002s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.003s +Ran 3 tests in 0.004s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.001s +Ran 3 tests in 0.002s OK ...E @@ -32925,28 +33023,28 @@ RuntimeError: Incomplete pickle support (__getstate_manages_dict__ not set) ---------------------------------------------------------------------- -Ran 4 tests in 0.004s +Ran 4 tests in 0.006s FAILED (errors=1) !!! TEST FAILURE: python UnitTestFeatMapUtils.py {} ....... ---------------------------------------------------------------------- -Ran 7 tests in 0.012s +Ran 7 tests in 0.019s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.014s +Ran 4 tests in 0.020s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 1.979s +Ran 4 tests in 3.636s OK .......... ---------------------------------------------------------------------- -Ran 10 tests in 0.036s +Ran 10 tests in 0.057s OK . @@ -32956,7 +33054,7 @@ OK .......... ---------------------------------------------------------------------- -Ran 10 tests in 0.003s +Ran 10 tests in 0.004s OK ....E @@ -32975,15 +33073,15 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 5 tests in 0.026s +Ran 5 tests in 0.051s FAILED (errors=1) !!! TEST FAILURE: python UnitTestGobbi.py {} -................[19:38:32] Molecule does not have explicit Hs. Consider calling AddHs() -[19:38:32] Molecule does not have explicit Hs. Consider calling AddHs() +................[16:06:10] Molecule does not have explicit Hs. Consider calling AddHs() +[16:06:10] Molecule does not have explicit Hs. Consider calling AddHs() ..... ---------------------------------------------------------------------- -Ran 21 tests in 4.734s +Ran 21 tests in 8.478s OK mol_197 @@ -32997,7 +33095,7 @@ Ran 1 test in 0.000s OK -...[19:38:33] +...[16:06:11] **** Pre-condition Violation @@ -33008,65 +33106,65 @@ . ---------------------------------------------------------------------- -Ran 4 tests in 0.016s +Ran 4 tests in 0.026s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 10.242s +Ran 2 tests in 17.217s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.085s +Ran 2 tests in 0.118s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.010s +Ran 3 tests in 0.015s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.017s +Ran 4 tests in 0.023s OK -.....[19:38:44] WARNING: not removing hydrogen atom without neighbors -[19:38:44] WARNING: not removing hydrogen atom without neighbors -[19:38:44] WARNING: not removing hydrogen atom without neighbors -[19:38:44] WARNING: not removing hydrogen atom without neighbors -[19:38:44] WARNING: not removing hydrogen atom without neighbors -[19:38:44] WARNING: not removing hydrogen atom without neighbors -[19:38:44] WARNING: not removing hydrogen atom without neighbors -[19:38:44] WARNING: not removing hydrogen atom without neighbors -[19:38:44] WARNING: not removing hydrogen atom without neighbors -[19:38:44] WARNING: not removing hydrogen atom without neighbors -[19:38:44] WARNING: not removing hydrogen atom without neighbors -[19:38:44] WARNING: not removing hydrogen atom without neighbors -[19:38:44] WARNING: not removing hydrogen atom without neighbors -[19:38:44] WARNING: not removing hydrogen atom without neighbors -[19:38:44] WARNING: not removing hydrogen atom without neighbors -[19:38:44] WARNING: not removing hydrogen atom without neighbors -[19:38:44] WARNING: not removing hydrogen atom without neighbors -[19:38:44] WARNING: not removing hydrogen atom without neighbors -[19:38:44] WARNING: not removing hydrogen atom without neighbors +.....[16:06:30] WARNING: not removing hydrogen atom without neighbors +[16:06:30] WARNING: not removing hydrogen atom without neighbors +[16:06:30] WARNING: not removing hydrogen atom without neighbors +[16:06:30] WARNING: not removing hydrogen atom without neighbors +[16:06:30] WARNING: not removing hydrogen atom without neighbors +[16:06:30] WARNING: not removing hydrogen atom without neighbors +[16:06:30] WARNING: not removing hydrogen atom without neighbors +[16:06:30] WARNING: not removing hydrogen atom without neighbors +[16:06:30] WARNING: not removing hydrogen atom without neighbors +[16:06:30] WARNING: not removing hydrogen atom without neighbors +[16:06:30] WARNING: not removing hydrogen atom without neighbors +[16:06:30] WARNING: not removing hydrogen atom without neighbors +[16:06:30] WARNING: not removing hydrogen atom without neighbors +[16:06:30] WARNING: not removing hydrogen atom without neighbors +[16:06:30] WARNING: not removing hydrogen atom without neighbors +[16:06:30] WARNING: not removing hydrogen atom without neighbors +[16:06:30] WARNING: not removing hydrogen atom without neighbors +[16:06:30] WARNING: not removing hydrogen atom without neighbors +[16:06:30] WARNING: not removing hydrogen atom without neighbors ..... ---------------------------------------------------------------------- -Ran 10 tests in 0.316s +Ran 10 tests in 0.491s OK -ssssss[19:38:45] No suitable metadata found. -.[19:38:45] No suitable metadata found. +ssssss[16:06:31] No suitable metadata found. +.[16:06:31] No suitable metadata found. ......s/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/Draw/__init__.py:237: DeprecationWarning: legacy DrawingOptions not translated for new drawing code, please update manually warnings.warn( ..... ---------------------------------------------------------------------- -Ran 19 tests in 0.323s +Ran 19 tests in 0.486s OK (skipped=7) sss. ---------------------------------------------------------------------- -Ran 4 tests in 0.654s +Ran 4 tests in 1.014s OK (skipped=3) sss @@ -33076,33 +33174,33 @@ OK (skipped=3) .......... ---------------------------------------------------------------------- -Ran 10 tests in 0.537s +Ran 10 tests in 0.931s OK -..[19:38:47] SMARTS Parse Error: syntax error while parsing: boromicacid -[19:38:47] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -[19:38:47] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -[19:38:47] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -[19:38:47] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -[19:38:47] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -[19:38:47] reaction has no reactants -[19:38:47] reaction has no products -[19:38:47] initialization failed -[19:38:47] reaction has no reactants -[19:38:47] reaction has no products +..[16:06:34] SMARTS Parse Error: syntax error while parsing: boromicacid +[16:06:34] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +[16:06:34] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +[16:06:34] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +[16:06:34] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +[16:06:34] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +[16:06:34] reaction has no reactants +[16:06:34] reaction has no products +[16:06:34] initialization failed +[16:06:34] reaction has no reactants +[16:06:34] reaction has no products . ---------------------------------------------------------------------- -Ran 3 tests in 0.021s +Ran 3 tests in 0.029s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.010s +Ran 4 tests in 0.014s OK .................... ---------------------------------------------------------------------- -Ran 20 tests in 0.109s +Ran 20 tests in 0.144s OK !!! TEST FAILURE: python UnitTestGraphDescriptors_2.py {} @@ -33114,11 +33212,12 @@ !!! TEST FAILURE: python test_list.py {'dir': 'Pharm2D'} -97% tests passed, 7 tests failed out of 208 +96% tests passed, 8 tests failed out of 208 -Total Test time (real) = 103.46 sec +Total Test time (real) = 223.90 sec The following tests FAILED: + 11 - pyBV (Failed) 22 - pyAlignment (Failed) 28 - pyDistGeom (Failed) 51 - pyDepictor (Failed) @@ -33129,7 +33228,7 @@ Errors while running CTest make[2]: *** [Makefile:94: test] Error 8 make[2]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' -dh_auto_test: error: cd obj-i686-linux-gnu && make -j16 test ARGS\+=--verbose ARGS\+=-j16 returned exit code 2 +dh_auto_test: error: cd obj-i686-linux-gnu && make -j7 test ARGS\+=--verbose ARGS\+=-j7 returned exit code 2 make[1]: [debian/rules:131: override_dh_auto_test] Error 25 (ignored) make[1]: Leaving directory '/build/reproducible-path/rdkit-202209.3' create-stamp debian/debhelper-build-stamp @@ -33139,7 +33238,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/rdkit-202209.3' dh_auto_install - cd obj-i686-linux-gnu && make -j16 install DESTDIR=/build/reproducible-path/rdkit-202209.3/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-i686-linux-gnu && make -j7 install DESTDIR=/build/reproducible-path/rdkit-202209.3/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202209.3 -B/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -33150,1382 +33249,1382 @@ /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DistanceGeometry --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DistanceGeometry/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ForceField --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ForceField/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Resemblance.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/ClusterVis.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Butina.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Murtagh.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Clusters.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/murtagh_test.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/ClusterUtils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Standardize.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/entropy.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/BitClusterer.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/BitRank.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/files.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/ModelPackage +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/ModelPackage/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/ModelPackage/PackageUtils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/ModelPackage/Packager.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/ModelPackage/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/ID3.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/BuildQuantTree.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/randomtest.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/DecTree.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/QuantTree.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/Forest.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/SigTree.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/TreeVis.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/TreeUtils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/BuildSigTree.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/CrossValidate.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/Tree.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/PruneTree.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/FindQuantBounds.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/DataUtils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/MLData.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/Transforms.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/Stats.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/SplitData.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/Quantize.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/CompositeRun.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/NaiveBayes +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/NaiveBayes/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/NaiveBayes/ClassificationModel.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/NaiveBayes/CrossValidate.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/NaiveBayes/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Scoring +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Scoring/Scoring.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Scoring/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Scoring/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/AnalyzeComposite.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/MLUtils +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/MLUtils/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/MLUtils/VoteImg.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/BuildComposite.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/GrowComposite.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/MatOps.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/KNNModel.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/DistFunctions.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/KNNClassificationModel.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/KNNRegressionModel.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/CrossValidate.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/EnrichPlot.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/ScreenComposite.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/architecture.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/Network.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/Trainers.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/NetNode.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/ActFuncs.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/CrossValidate.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors/MoleculeDescriptors.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors/Descriptors.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors/Parser.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors/CompoundDescriptors.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/BayesComposite.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/Composite.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/AdjustComposite.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/SLT +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/SLT/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/SLT/Risk.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/SLT/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/SimDivFilters +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/SimDivFilters/__pycache__ -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/SimDivFilters/SimilarityPickers.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/SimDivFilters/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/SimDivFilters/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Numerics --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Numerics/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/RDConfig.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Geometry -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Geometry/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataManip --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataManip/Metric --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataManip/Metric/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataManip/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmilesOutput.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SDSupply.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmilesSupply.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmartsRemover.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmilesDupeFilter.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmartsMolFilter.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/DbMolSupply.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/demo.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/DbPickleSupplier.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Output.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Node.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Supply.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Transform.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Filter.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Avalon --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Avalon/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/six.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/StorageUtils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbInfo.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbReport.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbModule.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/__pycache__ -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbConnection.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/StorageUtils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/__pycache__ -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbUtils.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbResultSet.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbInfo.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbModule.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/stringformat.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Qt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Qt/pidQt4.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Qt/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Qt/pidQt.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/ReportLab --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/ReportLab/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/ReportLab/pidReportLab.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/TK --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/TK/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/TK/pidTK.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Pyart --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Pyart/pidPyart.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Pyart/Fontmapping.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Pyart/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/WX +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/WX/pidWxDc.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/WX/pidWX.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/WX/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/fontinfo.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/pidPS.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/latin1MetricsCache.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/psmetrics.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/pidPS.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/fontinfo.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/latin1MetricsCache.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pidPIL.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-8.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-18.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-18.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/metrics.dat --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-24.pbm -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-24.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-12.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-24.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-24.pil -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-18.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-18.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-14.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-12.pil -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-8.pil.1 --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-12.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/removemedium.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-12.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-10.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-14.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-8.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/metrics.dat -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-8.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-8.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-8.pil.1 +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pbm -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-10.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-8.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-12.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-24.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-12.pil -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-10.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pil -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-14.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-12.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-14.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-18.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-8.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/removemedium.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-8.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-12.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-24.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-14.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-10.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-24.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-14.pil -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-24.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-14.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-18.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-14.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-10.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pil -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-18.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pbm -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-18.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-8.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-14.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/util --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/util/HTMLPiddler.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/util/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/pid.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/patches --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/patches/Imaging-1.1-fixplugin-path --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/patches/Imaging-1.1.1.diff --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/WX --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/WX/pidWxDc.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/WX/pidWX.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/WX/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pidPIL.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/stringformat.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/TK +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/TK/pidTK.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/TK/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/__pycache__ -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pidPDF.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pdfmetrics.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pdfutils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pdfgen.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pdfgeom.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pdfdoc.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pidPDF.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pdfgeom.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/colors.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/README +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pdfmetrics.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pdfgen.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/pagesizes.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/utils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/SVG --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/SVG/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/SVG/pidSVG.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/examples --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/examples/tkCanvasPIL-with-scrollbars.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/examples/tkCanvas-with-scrollbars.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/examples/formatted-strings.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/colors.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/testallps.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/testallps.ps --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/pstests.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/pidtest.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/testallps.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/__pycache__ -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/__pycache__/pidtest.cpython-311.pyc -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/__pycache__/pstests.cpython-311.pyc --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/RDConfig.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/pidtest.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/pstests.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/patches +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/patches/Imaging-1.1.1.diff +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/patches/Imaging-1.1-fixplugin-path +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/README +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/examples +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/examples/formatted-strings.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/examples/tkCanvas-with-scrollbars.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/examples/tkCanvasPIL-with-scrollbars.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/utils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/pid.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/ReportLab +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/ReportLab/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/ReportLab/pidReportLab.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/util +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/util/HTMLPiddler.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/util/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Pyart +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Pyart/Fontmapping.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Pyart/pidPyart.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Pyart/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Qt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Qt/pidQt4.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Qt/pidQt.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Qt/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/SVG +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/SVG/pidSVG.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/SVG/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Numerics +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Numerics/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/Sheridan.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/Torsions.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/Pairs.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/Utils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FragmentMatcher.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/Matcher.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/Generate.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/Utils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/Gobbi_Pharm2D.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/LazyGenerator.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/SigFactory.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolCatalog.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/DSViewer.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/nbtests +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/nbtests/ChEMBL_quinolones.tsv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/nbtests/rdkit-structure-renderer.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/nbtests/github4823.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FilterCatalog.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Suppliers --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Suppliers/DbMolSupplier.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Suppliers/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Suppliers/MolSupplier.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Suppliers/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Suppliers/MolSupplier.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Suppliers/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Suppliers/DbMolSupplier.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EnumerateHeterocycles.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fragments.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ShowMols.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolSurf.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/BRICS.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Descriptors3D.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/FingerprintUtils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/Loader_sa.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/Loader_orig.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/Loader.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Crippen.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/TemplateExpand.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/DescriptorUtilities.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/AlignDepict.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/SDFToCSV.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/BulkTester.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/PropertyMol.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FragmentCatalog.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/PandasPatcher.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/DSViewer.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Graphs.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Randomize.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Descriptors.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fraggle +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fraggle/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fraggle/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fraggle/FraggleSim.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/inchi.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/QED.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/cairoCanvas.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/similarityMap1_out2.svg --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/similarityMap1_out.svg --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/canvasbase.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/aggCanvas.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/mplCanvas.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/SimilarityMaps.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/FreeSans.ttf --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/MolDrawing.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/InteractiveRenderer.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/qtCanvas.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/SimilarityMaps.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/spingCanvas.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/mplCanvas.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/cairoCanvas.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/similarityMap1_out2.svg +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/qtCanvas.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/IPythonConsole.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/InteractiveRenderer.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/canvasbase.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/similarityMap1_out.svg +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/MolDrawing.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Descriptors3D.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Crippen.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FunctionalGroups.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/FeatMapUtils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/FeatMapParser.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/FeatMaps.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/FeatMapPoint.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/PropertyMol.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/SimpleEnum +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/SimpleEnum/__pycache__ -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/SimpleEnum/Enumerator.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/SimpleEnum/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/SimpleEnum/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Recap.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MCS.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Lipinski.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/SATIS.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/inchi.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/TemplateAlign.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Features --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Features/ShowFeats.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Features/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Features/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Features/FeatDirUtilsRD.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/RegistrationHash.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Graphs.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Scaffolds --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Scaffolds/ScaffoldNetwork.ipynb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Scaffolds/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Scaffolds/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Scaffolds/MurckoScaffold.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fraggle --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fraggle/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fraggle/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fraggle/FraggleSim.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AllChem.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FastSDMolSupplier.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/fmcs --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/fmcs/fmcs.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/fmcs/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/fmcs/fmcs --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/TorsionFingerprints.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Descriptors.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/PandasTools.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FragmentMatcher.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/__pycache__ -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/validations.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/normalize.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/tautomer.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/standardize.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/charge.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/utils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/fragment.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/__pycache__ -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/test_standardizer.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/errors.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/resonance.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/tautomer.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/metal.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/utils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/errors.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/normalize.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/validate.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/resonance.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/FeatMapParser.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/FeatMapPoint.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/FeatMapUtils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/FeatMaps.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/GraphDescriptors.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/fragment.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Lipinski.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Features +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Features/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Features/ShowFeats.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Features/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Features/FeatDirUtilsRD.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/SaltRemover.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FastSDMolSupplier.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Recap.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/Pairs.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/Torsions.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/Sheridan.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/Utils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/BuildFragmentCatalog.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MCS.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemicalFeatures.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolCatalog.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatFinderCLI.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/PyMol.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/Loader_sa.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/Loader.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/Loader_orig.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/FingerprintUtils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/TemplateAlign.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EnumerateStereoisomers.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolKey +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolKey/MolKey.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolKey/InchiInfo.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolKey/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/BuilderUtils.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/SubshapeObjects.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/testCombined.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/__pycache__ -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/SubshapeBuilder.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/BuilderUtils.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/SubshapeAligner.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/testCombined.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/TemplateExpand.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/SDFToCSV.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/BulkTester.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/AlignDepict.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/DescriptorUtilities.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/Matcher.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/Gobbi_Pharm2D.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/Generate.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/SigFactory.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/LazyGenerator.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/Utils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AllChem.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ReducedGraphs.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D/ExcludedVolume.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D/EmbedLib.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D/Pharmacophore.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EnumerateStereoisomers.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ReducedGraphs.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EnumerateHeterocycles.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D/Pharmacophore.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D/ExcludedVolume.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/GraphDescriptors.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/PandasTools.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Scaffolds +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Scaffolds/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Scaffolds/ScaffoldNetwork.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Scaffolds/MurckoScaffold.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Scaffolds/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/RegistrationHash.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/PandasPatcher.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/SATIS.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/DbFpSupplier.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/SimilarityScreener.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/FingerprintMols.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/MolSimilarity.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/__pycache__ -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/ClusterMols.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/SimilarityScreener.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/DbFpSupplier.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/BuildFragmentCatalog.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/MolSimilarity.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemicalForceFields.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Randomize.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/SaltRemover.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/nbtests --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/nbtests/github4823.ipynb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/nbtests/rdkit-structure-renderer.ipynb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/nbtests/ChEMBL_quinolones.tsv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/fmcs +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/fmcs/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/fmcs/fmcs.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/fmcs/fmcs -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EState --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EState/EState_VSA.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EState/Fingerprinter.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EState/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EState/EState_VSA.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EState/EState.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EState/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EState/AtomTypes.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EState/EState.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EState/__pycache__ -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MACCSkeys.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FunctionalGroups.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/QED.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ShowMols.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolKey --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolKey/MolKey.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolKey/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolKey/InchiInfo.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemicalFeatures.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolSurf.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatFinderCLI.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fragments.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FilterCatalog.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FragmentCatalog.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/TorsionFingerprints.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/RDLogger.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/listutils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/fileutils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/chemutils.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/cactvs.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/chemdraw.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/spiral.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/chemdraw_qax.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/comhack.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/listutils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/fileutils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/chemdraw.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/chemdraw_qax.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/retest.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/chemutils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/RDLogger.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataManip +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataManip/Metric +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataManip/Metric/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataManip/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DistanceGeometry +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DistanceGeometry/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/BitEnsemble.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/TopNContainer.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/BitEnsembleDb.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/BitUtils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/TopNContainer.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/LazySignature.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/BitEnsembleDb.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/VectCollection.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/__pycache__ -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/HierarchyVis.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/GrowComposite.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Scoring --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Scoring/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Scoring/Scoring.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Scoring/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/NaiveBayes --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/NaiveBayes/CrossValidate.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/NaiveBayes/ClassificationModel.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/NaiveBayes/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/NaiveBayes/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/AnalyzeComposite.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/SLT --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/SLT/Risk.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/SLT/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/SLT/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/ModelPackage --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/ModelPackage/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/ModelPackage/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/ModelPackage/PackageUtils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/ModelPackage/Packager.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors/MoleculeDescriptors.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors/CompoundDescriptors.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors/Descriptors.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors/Parser.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/Network.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/CrossValidate.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/architecture.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/Trainers.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/ActFuncs.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/NetNode.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/Quantize.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/FindQuantBounds.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/Stats.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/MLData.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/DataUtils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/SplitData.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/Transforms.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/CompositeRun.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/BuildComposite.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/ClusterVis.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/ClusterUtils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Resemblance.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/murtagh_test.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Murtagh.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Standardize.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Butina.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Clusters.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/ScreenComposite.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/CrossValidate.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/KNNModel.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/KNNRegressionModel.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/KNNClassificationModel.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/DistFunctions.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/MLUtils --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/MLUtils/VoteImg.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/MLUtils/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/files.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/MatOps.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/BayesComposite.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/Composite.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/AdjustComposite.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/BitRank.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/entropy.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/BitClusterer.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/TreeUtils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/CrossValidate.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/DecTree.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/SigTree.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/PruneTree.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/QuantTree.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/Tree.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/BuildQuantTree.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/BuildSigTree.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/ID3.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/Forest.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/randomtest.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/TreeVis.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/EnrichPlot.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/BitEnsemble.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/VectCollection.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/six.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/RDRandom.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Avalon +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Avalon/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmartsRemover.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/DbMolSupply.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/demo.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmilesDupeFilter.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/DbPickleSupplier.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SDSupply.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmartsMolFilter.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmilesOutput.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmilesSupply.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Filter.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Output.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Transform.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Supply.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Node.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/TestRunner.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ForceField +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ForceField/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Crippen.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts/font_dumper.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts/amadeus_font_license.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts/Amadeus.ttf +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts/Telex-Regular.ttf +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts/telex_font_license.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts/roboto_regular_license.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Salts.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/SmartsLib +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/RLewis_smarts.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/patty_rules.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/fps.1000.counts.pkl.gz +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/mols.1000.pkl.gz +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/bench2.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/struchk +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.chk -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.trn -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.opt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.chk --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data/wehi_mols.csv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data/test_set3.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data/run_tests.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains/wehi_pains.csv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains/README.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/BaseFeatures.fdef -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/NCI -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/NCI/first_200.props.sdf --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/NCI/first_5k.tpsa.csv -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/NCI/first_5K.smi +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/NCI/first_5k.tpsa.csv -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/NCI/first_200.tpsa.csv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Functional_Group_Hierarchy.txt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/RDData.sqlt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/SmartsLib --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/RLewis_smarts.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/patty_rules.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/fps.1000.counts.pkl.gz --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/mols.1000.pkl.gz --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/bench2.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/rddata.sql +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/FragmentDescriptors.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/RDTests.sqlt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Crippen.txt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/DTDs --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Dataset.dtd -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Model.dtd +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Dataset.dtd -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/DTDs/validate.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/BaseFeatures.fdef --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts/font_dumper.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts/Amadeus.ttf --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts/roboto_regular_license.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts/Telex-Regular.ttf --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts/amadeus_font_license.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts/telex_font_license.txt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/FunctionalGroups.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Salts.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/FragmentDescriptors.csv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/rddata.sql --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/RDTests.sqlt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Functional_Group_Hierarchy.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains/README.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains/wehi_pains.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data/test_set3.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data/run_tests.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data/wehi_mols.csv -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_and_expand.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_cis_base.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_or_base.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_or2_base.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_trans_base.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_and2_base.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_cis_expand.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_and_base.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_and2_expand.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_cis_base.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_trans_expand.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_trans_base.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/CIPLabeling.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.ai +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.jpg +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.jpg +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.ai +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/FragmentCatalogs.html +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/SGroups.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/CodingStandards.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/EnhancedStereo.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/gsocGeneralFileReader.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/RD.css +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-MutipleCores.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GA.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-StereoChemTest.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-RingSubstitution.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-Tests.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/compounds.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GenericCores.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-example-lactam.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-DummyCores.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/MolStandardize.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/FingerprintGenerators.ipynb -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/An_overview_of_the_RDKit_jp.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Supplementary_Text_jp.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/RDKit_cookbook_jp.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/introduction_jp.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Getting_Started_with_RDKit_in_Python_jp.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Makefile --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/conf.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_Book_jp.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/terminology_jp.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/RDKit_cookbook_jp.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Supplementary_Text_jp.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Installation_jp.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Backwards_incompatible_changes_jp.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/index.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_Book_jp.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Backwards_incompatible_changes_jp.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_database_cartridge_jp.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Installation_jp.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Makefile +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/An_overview_of_the_RDKit_jp.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/conf.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_19.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_55.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_30.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_40.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_34.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_31.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_33.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_15.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_17.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_38.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_28.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_46.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_32.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_49.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_12.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_44.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_2.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_50.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_48.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_36.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_16.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_8.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_37.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_44.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_22.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_33.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_31.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_34.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_27.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_19.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_47.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_48.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_54.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_60.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_15.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_20.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_58.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_23.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_61.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_52.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_36.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_49.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_7.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_39.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_29.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_53.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_41.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_25.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_5.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_26.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_57.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_35.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_2.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_18.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_6.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_14.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_24.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_13.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_11.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_59.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_27.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_43.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_9.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_45.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_28.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_8.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_35.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_52.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_4.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_39.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_32.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_57.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_61.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_25.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_40.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_56.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_14.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_26.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_51.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_62.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_47.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_42.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_17.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_38.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_30.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_45.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_10.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_56.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_12.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_21.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_3.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_4.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_37.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_20.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_9.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_7.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_62.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_24.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_5.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_23.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_43.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_6.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_55.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_29.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_18.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_22.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_41.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_58.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_60.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_21.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/ForceFieldTerms.new.odt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/UFF Parameters.ods -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_CorrMat.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_Correlation.csv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_Correlation.csv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/README -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_CorrMat.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_Correlation.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/README +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_Correlation.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_CorrMat.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_Correlation.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/UFF Parameters.ods +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/ForceFieldTerms.new.odt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp4.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond3.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_11.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_3.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_23_im1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_10.jpg --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im2.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_7.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/indole1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im0.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im0.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/query_bonds.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_3_im0.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_22_im1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molE.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/parastereo_1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/rdk_bit1553.svg --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_8_im0.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_3.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/rdk_bit1553_2.svg --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond2.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im2.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_29_im0.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im2.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_2_im0.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_10.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_2.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_ex2.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molF.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_charges.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im4.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im0.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_2_im1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_28_im1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/query_bonds.2.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mfp2_bit872.svg --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_3.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp3.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp3.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_32_im1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/stereo_annotation.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_4.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im5.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_8.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp2.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_30_im1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_mol2.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_13_im1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_crippen.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im3.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_9.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_2.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im0.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_oh2.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_13_im0.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/substruct_search_parameters1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im0.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_2.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_30_im0.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im2.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im6.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_35_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp3.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/query_bonds.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_32_im0.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/reaction1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_5.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im4.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mol_metadata1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_10.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/stereo_annotation.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/ary_group.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im3.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_28_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_20_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_ex1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_10.jpg +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_7.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im5.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/query_atoms.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_tb1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_29_im0.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_22_im0.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_annotation_1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_oh1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molF.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp4.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_13_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_36_im0.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im3.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_5.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mfp2_bit872.svg +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_36_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im3.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_17_im0.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_20_im1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp2.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_19_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_13_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_tb2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im2.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_6.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_36_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_32_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molB.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_3.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_oh2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_19_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molA.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/indole1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_tb1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_2_im1.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_molgrid.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im2.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/parastereo_2.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_mol1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_11.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond3.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molE.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_2.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molD.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im0.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_rf.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_17_im1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_36_im1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mol_metadata1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_charges.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im2.svg --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/reaction1_highlight.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molC.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_ex1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_9.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_mol1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_molgrid_aligned.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im2.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molG.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/ary_group.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_12.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molA.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_23_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/parastereo_1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im4.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im2.svg +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im1.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_28_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_mol2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_3.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/rdk_bit1553_2.svg +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_8.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_22_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_oh1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im6.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_23_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/parastereo_2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp3.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_3.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_30_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molG.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im5.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_17_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_3_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_annotation_1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/reaction1_highlight.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/substruct_search_parameters1.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im0.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molB.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_20_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_4.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_rf.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_ex2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_12.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_8_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/reaction1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im0.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_missing1.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_tb2.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_molgrid_aligned.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_35_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/query_atoms.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_crippen.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_30_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molC.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_20_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/rdk_bit1553.svg +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/query_bonds.2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_2_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/RDKit_Book.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/Install.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/Overview.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/README.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/AmideBond.rxn +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/s1p_chembldoc89753.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/input.mol +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf.gz +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/test_multi_colours.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/solubility.train.sdf +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/chiral.mol +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/5ht3ligs.sdf +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/cdk2.sdf +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/MinimalFeatures.fdef +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/solubility.test.sdf +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/bzr.sdf +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/invalid.mol +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/bzr.smi -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/api-docs.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/BackwardsIncompatibleChanges.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/Cartridge.md -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example4.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example2.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example3.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example10.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example14.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example6.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example1.cpp -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example12.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example8.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/FindMyRDKit.cmake +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example14.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example11.cpp -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example15.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example2.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example8.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example13.cpp -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example9.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example11.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/CMakeLists.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/FindMyRDKit.cmake --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example1.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example3.cpp -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example16.cpp -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example17.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example7.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example13.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example4.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/CMakeLists.txt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example5.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/GettingStartedInPython.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/Cartridge.md --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/RDKit_Book.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example7.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example10.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example6.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/index.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/GettingStartedInC++.md --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/Install.md -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/exts -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/exts/extapi.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/Makefile --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/conf.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/BackwardsIncompatibleChanges.md -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.utils.chemutils.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.EState.Fingerprinter.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdMolTransforms.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.SimpleEnum.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.SimDivFilters.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ChemUtils.DescriptorUtilities.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolDb.Loader.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FeatMaps.FeatMapPoint.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.inchi.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Neural.CrossValidate.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.Supply.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DistanceGeometry.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdMolDescriptors.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.DecTree.TreeVis.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.aggCanvas.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.EnumerateHeterocycles.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.IPythonConsole.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.ModelPackage.Packager.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FastSDMolSupplier.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FragmentMatcher.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolDb.Loader_sa.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Geometry.rdGeometry.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.NaiveBayes.CrossValidate.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolStandardize.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Fraggle.FraggleSim.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm2D.Matcher.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Fingerprints.MolSimilarity.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolDb.Loader_orig.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.KNN.KNNClassificationModel.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdFreeSASA.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.BuildFragmentCatalog.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.CompositeRun.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/modules.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DistanceGeometry.DistGeom.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Features.ShowFeats.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.SimDivFilters.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.DecTree.PruneTree.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Subshape.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm2D.SigFactory.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Neural.ActFuncs.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Fingerprints.SimilarityScreener.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm3D.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataManip.Metric.rdMetricMatrixCalc.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.rdMolDraw2DQt.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.GrowComposite.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataStructs.LazySignature.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.RegistrationHash.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdtrajectory.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.AtomPairs.Utils.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.SimDivFilters.SimilarityPickers.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Data.DataUtils.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Fingerprints.FingerprintMols.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Descriptors.Descriptors.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Neural.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolDb.Loader_orig.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdCoordGen.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Fingerprints.DbFpSupplier.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdAbbreviations.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.SmilesOutput.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.DecTree.DecTree.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Scaffolds.MurckoScaffold.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdinchi.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DistanceGeometry.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdShapeHelpers.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.Filter.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Avalon.pyAvalonTools.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdReducedGraphs.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.SDSupply.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataStructs.VectCollection.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.InfoTheory.BitRank.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ChemicalForceFields.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Randomize.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.TorsionFingerprints.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.AtomPairs.Pairs.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Crippen.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Dbase.DbReport.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdChemicalFeatures.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolDb.Loader_sa.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.AnalyzeComposite.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdMolCatalog.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdSubstructLibrary.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdEHTTools.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdMolInterchange.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Dbase.DbResultSet.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdchem.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Scoring.Scoring.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm2D.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Descriptors.CompoundDescriptors.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Avalon.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.DecTree.CrossValidate.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MCS.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.IPythonConsole.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.utils.cactvs.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.TestRunner.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Cluster.ClusterUtils.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdmolops.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Fingerprints.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.AtomPairs.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.DecTree.BuildQuantTree.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.QED.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Data.Transforms.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.Output.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Recap.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Data.SplitData.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FilterCatalog.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataStructs.BitUtils.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.DecTree.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataManip.Metric.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.MolDrawing.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ChemUtils.BulkTester.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.RDPaths.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.qtCanvas.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataStructs.BitEnsemble.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Numerics.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ForceField.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.SmartsRemover.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdfragcatalog.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.inchi.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.SLT.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.DbMolSupply.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm3D.ExcludedVolume.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.EState.EState.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.InfoTheory.BitClusterer.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Dbase.DbInfo.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Fingerprints.SimilarityScreener.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.SmilesDupeFilter.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.utils.listutils.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Suppliers.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ForceField.rdForceField.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.ModelPackage.PackageUtils.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdPartialCharges.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Graphs.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.KNN.CrossValidate.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.utils.spiral.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdfiltercatalog.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.RDRandom.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.utils.chemutils.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdMolAlign.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm3D.Pharmacophore.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Composite.BayesComposite.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.SLT.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.SimDivFilters.rdSimDivPickers.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.SimpleEnum.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolDb.FingerprintUtils.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Dbase.DbModule.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.InfoTheory.BitClusterer.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.cairoCanvas.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.DbPickleSupplier.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolKey.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdForceFieldHelpers.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.SmilesSupply.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.DbMolSupply.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.PeriodicTable.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.ModelPackage.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.files.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdMolChemicalFeatures.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.ModelPackage.Packager.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Data.Quantize.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FastSDMolSupplier.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdAbbreviations.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataStructs.BitEnsemble.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdTautomerQuery.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdFingerprintGenerator.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Subshape.BuilderUtils.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.SmartsMolFilter.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.PyMol.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.EState.AtomTypes.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolCatalog.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.InfoTheory.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.EnrichPlot.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Scaffolds.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.PropertyMol.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Dbase.DbConnection.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Descriptors.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Scaffolds.rdScaffoldNetwork.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.MLUtils.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.RDConfig.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdPartialCharges.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.EState.EState.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Scoring.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdMolInterchange.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Data.MLData.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.canvasbase.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Cluster.Butina.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.MolDrawing.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Dbase.DbInfo.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ShowMols.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.AtomPairs.Utils.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.AllChem.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdMolHash.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm2D.Generate.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.DecTree.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.KNN.KNNClassificationModel.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.KNN.KNNRegressionModel.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.ScreenComposite.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.KNN.DistFunctions.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.PyMol.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Composite.BayesComposite.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.DecTree.CrossValidate.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.SimpleEnum.Enumerator.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Fragments.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataStructs.VectCollection.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.MLUtils.VoteImg.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Descriptors3D.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Scoring.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Descriptors.MoleculeDescriptors.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.MLUtils.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Dbase.DbConnection.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.AnalyzeComposite.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.mplCanvas.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm3D.EmbedLib.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Fraggle.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.SDSupply.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.PropertyMol.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdDeprotect.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Cluster.Resemblance.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.EState.Fingerprinter.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FunctionalGroups.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.DecTree.TreeVis.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Cluster.Clustering.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ChemUtils.DescriptorUtilities.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MCS.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.Transform.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Crippen.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.SmartsMolFilter.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdSLNParse.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.DecTree.ID3.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.PeriodicTable.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Descriptors.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdMHFPFingerprint.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolCatalog.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Descriptors.Parser.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataManip.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdfragcatalog.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Subshape.SubshapeAligner.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdChemReactions.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.EState.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Subshape.SubshapeObjects.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.DecTree.SigTree.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Fingerprints.FingerprintMols.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm2D.Utils.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.EState.EState_VSA.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdMMPA.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.rdMolDraw2D.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.fmcs.fmcs.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Composite.Composite.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.SLT.Risk.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.canvasbase.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdMolChemicalFeatures.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Randomize.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Cluster.Standardize.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm2D.SigFactory.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm2D.Gobbi_Pharm2D.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Subshape.SubshapeBuilder.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.RDRandom.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Data.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Fingerprints.ClusterMols.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.NaiveBayes.CrossValidate.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.EnumerateStereoisomers.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Geometry.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdqueries.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Numerics.rdAlignment.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolKey.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataStructs.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdMHFPFingerprint.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.PandasTools.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.CompositeRun.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.NaiveBayes.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.BuildFragmentCatalog.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Suppliers.MolSupplier.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdCIPLabeler.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolDb.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Neural.NetNode.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.DecTree.Tree.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FeatMaps.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdDistGeom.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.RegistrationHash.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdShapeHelpers.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.Node.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.TemplateAlign.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ChemUtils.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.InfoTheory.entropy.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.RDConfig.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdSLNParse.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ChemUtils.BulkTester.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.MatOps.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Suppliers.DbMolSupplier.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm3D.EmbedLib.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.rdMolDraw2DQt.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Features.ShowFeats.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Data.FindQuantBounds.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Geometry.rdGeometry.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Suppliers.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdMolDescriptors.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Avalon.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.EnrichPlot.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.utils.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FilterCatalog.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.KNN.KNNModel.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Cluster.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolStandardize.rdMolStandardize.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.files.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataStructs.BitUtils.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm2D.Gobbi_Pharm2D.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.BRICS.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm2D.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.rdBase.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FragmentCatalog.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.utils.fileutils.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdRGroupDecomposition.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.RDLogger.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.SmilesOutput.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Dbase.StorageUtils.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FeatMaps.FeatMaps.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.SimilarityMaps.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.KNN.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Neural.Trainers.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.EState.EState_VSA.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.DecTree.BuildSigTree.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.DecTree.ID3.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.mplCanvas.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.qtCanvas.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ChemUtils.TemplateExpand.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.DecTree.TreeUtils.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Fragments.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.KNN.DistFunctions.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Data.Stats.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Subshape.BuilderUtils.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Descriptors3D.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Cluster.Clusters.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdtrajectory.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataManip.Metric.rdMetricMatrixCalc.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Descriptors.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.AllChem.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Scaffolds.rdScaffoldNetwork.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ForceField.rdForceField.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.DecTree.Tree.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ChemUtils.AlignDepict.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.ModelPackage.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.SaltRemover.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdMolCatalog.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.PandasTools.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.six.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.GraphDescriptors.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.BuildComposite.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Data.FindQuantBounds.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.fmcs.fmcs.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Geometry.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdMolEnumerator.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Cluster.Butina.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Neural.Network.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.KNN.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Neural.CrossValidate.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.fmcs.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Features.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.TemplateAlign.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.QED.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FeatMaps.FeatMapPoint.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.TestRunner.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdFMCS.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdSubstructLibrary.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Dbase.DbUtils.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Cluster.ClusterUtils.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolDb.Loader.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Composite.AdjustComposite.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Neural.ActFuncs.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdDepictor.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ChemicalForceFields.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataStructs.TopNContainer.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm2D.Utils.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Neural.NetNode.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.fmcs.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.utils.cactvs.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.SATIS.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.AtomPairs.Sheridan.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolKey.InchiInfo.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.SmartsRemover.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdFMCS.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Descriptors.MoleculeDescriptors.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Neural.Network.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Cluster.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdTautomerQuery.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdmolops.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdFingerprintGenerator.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Suppliers.MolSupplier.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.NaiveBayes.ClassificationModel.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.TorsionFingerprints.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.DecTree.Forest.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Numerics.rdAlignment.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.DecTree.QuantTree.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.SimDivFilters.SimilarityPickers.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ChemUtils.SDFToCSV.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FeatMaps.FeatMapUtils.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdDistGeom.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Recap.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.Output.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Dbase.StorageUtils.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.DecTree.TreeUtils.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdReducedGraphs.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.ModelPackage.PackageUtils.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Dbase.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataStructs.cDataStructs.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.SimDivFilters.rdSimDivPickers.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Subshape.SubshapeAligner.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Descriptors.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Composite.Composite.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ChemUtils.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Scoring.Scoring.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.utils.listutils.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Descriptors.CompoundDescriptors.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FeatMaps.FeatMaps.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataStructs.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.SLT.Risk.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Lipinski.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.InfoTheory.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FeatFinderCLI.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Descriptors.Parser.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ChemUtils.AlignDepict.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.utils.spiral.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdFreeSASA.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Dbase.DbUtils.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DistanceGeometry.DistGeom.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Data.cQuantize.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.ScreenComposite.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.BuildComposite.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FragmentMatcher.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdCoordGen.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdDeprotect.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.rdMolDraw2D.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.AtomPairs.Torsions.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.EnumerateStereoisomers.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Features.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Data.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdCIPLabeler.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Features.FeatDirUtilsRD.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.InfoTheory.BitRank.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolKey.InchiInfo.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdChemicalFeatures.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.InfoTheory.rdInfoTheory.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Fingerprints.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdchem.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.DecTree.SigTree.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.EState.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Cluster.Murtagh.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm3D.Pharmacophore.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Avalon.pyAvalonTools.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Cluster.ClusterVis.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.SmilesSupply.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdqueries.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Dbase.DbResultSet.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.Node.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.InfoTheory.entropy.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataManip.Metric.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Data.Stats.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Scaffolds.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ReducedGraphs.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Cluster.Clustering.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.GrowComposite.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Lipinski.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FeatMaps.FeatMapUtils.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataStructs.TopNContainer.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ChemicalFeatures.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Scaffolds.MurckoScaffold.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ForceField.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FragmentCatalog.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataStructs.LazySignature.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Graphs.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.DbPickleSupplier.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm3D.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Dbase.DbModule.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Subshape.SubshapeBuilder.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.MatOps.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ChemUtils.SDFToCSV.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.NaiveBayes.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ChemUtils.TemplateExpand.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.DecTree.BuildQuantTree.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MACCSkeys.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FunctionalGroups.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FeatMaps.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolDb.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Dbase.DbReport.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FeatMaps.FeatMapParser.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Neural.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Data.MLData.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolSurf.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Fingerprints.DbFpSupplier.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.EnumerateHeterocycles.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdMolHash.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolKey.MolKey.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdinchi.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolStandardize.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm2D.Matcher.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Fraggle.FraggleSim.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdDepictor.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataStructs.cDataStructs.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.cairoCanvas.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Numerics.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/modules.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.six.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.DataStructs.BitEnsembleDb.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.Transform.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MACCSkeys.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.aggCanvas.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Cluster.ClusterVis.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdmolfiles.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.InfoTheory.rdInfoTheory.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Data.Quantize.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolSurf.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Data.SplitData.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.ChemicalFeatures.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.EState.AtomTypes.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Composite.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.RDPaths.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.BRICS.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.KNN.CrossValidate.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolDb.FingerprintUtils.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Draw.SimilarityMaps.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.GraphDescriptors.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.NaiveBayes.ClassificationModel.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.AtomPairs.Torsions.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Pharm2D.Generate.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.DecTree.DecTree.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Subshape.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Data.DataUtils.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.SaltRemover.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdfiltercatalog.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Dbase.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.SimpleEnum.Enumerator.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdRGroupDecomposition.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Cluster.Murtagh.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolStandardize.rdMolStandardize.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.utils.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.utils.fileutils.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.DecTree.Forest.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.KNN.KNNRegressionModel.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.DecTree.PruneTree.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Features.FeatDirUtilsRD.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.SATIS.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.rdBase.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Neural.Trainers.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/input.mol --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/5ht3ligs.sdf --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/s1p_chembldoc89753.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf.gz --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/bzr.sdf --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/solubility.test.sdf --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/solubility.train.sdf --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/test_multi_colours.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/AmideBond.rxn --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/invalid.mol --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/cdk2.sdf --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/bzr.smi --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/chiral.mol --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/README.md --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/MinimalFeatures.fdef --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/Overview.md --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/index.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-Tests.ipynb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GenericCores.ipynb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-example-lactam.ipynb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/FingerprintGenerators.ipynb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/MolStandardize.ipynb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-RingSubstitution.ipynb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/compounds.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-MutipleCores.ipynb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GA.ipynb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-StereoChemTest.ipynb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-DummyCores.ipynb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/RD.css +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Data.cQuantize.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.VLib.NodeLib.SmilesDupeFilter.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdmolfiles.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Suppliers.DbMolSupplier.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdChemReactions.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdMMPA.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Subshape.SubshapeObjects.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.ML.Data.Transforms.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.Fingerprints.ClusterMols.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.AtomPairs.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.rdEHTTools.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.MolKey.MolKey.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/GettingStartedInPython.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/conf.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Images +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Images/logo.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Images/wiki -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Images/wiki/morganfp_atomenv1.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Images/logo_plain.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Images/logo.inkscape.svg --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Images/logo.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Images/logo.ai --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Images/logo_plain.inkscape.svg -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Images/logo.lrg.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_trans_expand.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_and_expand.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_and2_base.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_or_base.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_trans_base.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_and2_expand.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_or2_base.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_cis_base.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_and_base.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_cis_expand.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_cis_base.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_trans_base.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/CodingStandards.md --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/CIPLabeling.md --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/SGroups.md --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.jpg --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/FragmentCatalogs.html --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.jpg --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.ai --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.ai --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/gsocGeneralFileReader.md --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/EnhancedStereo.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Images/logo_plain.inkscape.svg +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Images/logo.ai -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/pytest.ini --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/test --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/test/test_freewilson.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/freewilson.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/requirements.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/setup.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810_scaffold.mol --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810_act.csv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810.smi --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/README.md --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/readme.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/atomcontrib.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/rdkit_tversky.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/cxn_tversky.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/final_fraggle_results.csv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query.smi --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/ChEMBL_11265_actives.smi --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/fragmentation_tversky_out --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query_fragmentation.csv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/fraggle.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/SubstructureFilter_HitTriaging_wPubChemExamples.csv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/FilterSet_NIBR2019_wPubChemExamples.html --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/assignSubstructureFilters.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/filterExamples.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples/chembl24_structs_randomtestSample_100_out.csv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples/chembl24_structs_randomtestSample_100.csv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/README.md --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered_parse.tsv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered.tsv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fastcluster.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/cdk2.smi --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fp.tsv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/centroid.tsv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/README.md --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/sdf2smi.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/converted.smi --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/cdk2.sdf --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/ChiralDescriptors.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/README.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NP_Score +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NP_Score/publicnp.model.gz +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NP_Score/npscorer.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NP_Score/README +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/identifyReactants.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/utils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/README.txt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/pzc -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/pzc/readme.md --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/pzc/p_con.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/pzc/p_con.html +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/pzc/p_con.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/fpscores.pkl.gz +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data/zim.100.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/UnitTestSAScore.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/README +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/sascorer.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/BEG.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/1C9.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/AKI.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/5dpv_complex.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/6c83_complex.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/N15.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/JVE.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/CalcLigRMSD.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/Examples_CalcLigRMSD.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/README.md -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/aurka_protein_2c6e.pdb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_1.pdb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/5dpv.pdb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_JVE_pH74_netcharge1.pdb -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/JVE_renamed.pdb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/BEG_test.pdb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_ACP_pH74_netcharge1.pdb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1d4i_BEG.pdb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/6c83.pdb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_renamed.pdb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/N15_renamed.pdb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4i23_1C9.pdb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_3w2p_1C9_pH74_netcharge1.pdb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_SKE_pH74_netcharge1.pdb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/AKI_renamed.pdb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_crystal_aligned_1.pdb -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4i24_1C9.pdb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/crystal_aligned.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_JVE_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/5dt0.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/5dpv.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/6c83.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/lig_crystal_aligned.pdb -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3w2c_N15.pdb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/BEG_test.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_1.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4i23_1C9.pdb -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4uzh_JVE.pdb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/lig_crystal_aligned.pdb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_N15_pH74_netcharge1.pdb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_2.pdb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/5dt0.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_AKI_pH74_netcharge1.pdb -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3m11_AKI.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/crystal_aligned.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_ACP_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_crystal_aligned_1.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/aurka_protein_2c6e.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1d4i_BEG.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_3w2p_1C9_pH74_netcharge1.pdb -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1C9_renamed.pdb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_AKI_pH74_netcharge1.pdb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/README.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/N15_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_2.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_N15_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/AKI_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_SKE_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/CalcLigRMSD.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/AKI.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/BEG.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/5dpv_complex.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/1C9.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/6c83_complex.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/N15.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/JVE.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/Examples_CalcLigRMSD.ipynb -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/LEF --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePredict.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/LEF/README.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePlot.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/LEF/ClusterFps.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/LEF/CreateFps.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePredict.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/LEF/AddLabels.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Glare --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Glare/README.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Glare/glare.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/README.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/identifyReactants.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/utils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.h --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/CMakeLists.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/test.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/test_list.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/rdConformerParser.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/CMakeLists.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/test_list.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/testConformerParser.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/LEF/ClusterFps.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePlot.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/LEF/README.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/IFG +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/IFG/README +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/IFG/ifg.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/README.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/test +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/test/test_freewilson.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/pytest.ini +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810_act.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810.smi +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810_scaffold.mol +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/freewilson.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/requirements.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/setup.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/README.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered_parse.tsv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fastcluster.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/cdk2.smi +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/sdf2smi.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/cdk2.sdf +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/converted.smi +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fp.tsv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered.tsv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/centroid.tsv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/README.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/SubstructureFilter_HitTriaging_wPubChemExamples.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/assignSubstructureFilters.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/filterExamples.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples/chembl24_structs_randomtestSample_100_out.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples/chembl24_structs_randomtestSample_100.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/FilterSet_NIBR2019_wPubChemExamples.html +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/pbf.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/demo.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.h +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/testData +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.sdf +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.out +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/README +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/Makefile -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/search_mmp_db.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/README.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/mol_transform.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/test_list.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/cansmirk.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs_smarts.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym_maxheavy.csv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxratio.csv -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_output.txt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_transfroms.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_smart_output.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample.smi --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mol_trans_output.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxheavy.csv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smiles_mol_trans.smi -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_fragmented.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_smarts_output.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_smi_output.txt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_default.csv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxratio.csv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans_smarts.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_smi.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/simple.smi --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_cansmirks.txt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample.smi +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym_maxheavy.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_smart_output.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_smi.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_output.txt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks_mol_trans.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans_smarts.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_cansmirks.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs_smarts.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxheavy.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mol_trans_output.txt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_output.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_smi_output.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/cansmirk.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/rfrag.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smiles_mol_trans.smi +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_smarts_output.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/simple.smi -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/test_rfrag.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/mol_transform.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/test_list.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/search_mmp_db.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/create_mmp_db.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/README.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/rfrag.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/indexing.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/README --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data/zim.100.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/fpscores.pkl.gz --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/UnitTestSAScore.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/sascorer.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CMakeLists.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NP_Score --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NP_Score/README --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NP_Score/publicnp.model.gz --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NP_Score/npscorer.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/README.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/ChiralDescriptors.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/pbf.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/Makefile --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/README --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.h --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/testData --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.sdf --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.out --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/demo.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/Frames.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/README --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/BaseFeatures_DIP2_NoMicrospecies.fdef --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/IFG --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/IFG/ifg.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/IFG/README -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/MolVS -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/MolVS/molvs_cli.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/BaseFeatures_DIP2_NoMicrospecies.fdef +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/README +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/Frames.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CMakeLists.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Glare +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Glare/glare.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Glare/README.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query.smi +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/fragmentation_tversky_out +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/ChEMBL_11265_actives.smi +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query_fragmentation.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/final_fraggle_results.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/fraggle.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/atomcontrib.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/readme.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/rdkit_tversky.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/cxn_tversky.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/rdConformerParser.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/test_list.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/CMakeLists.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/testConformerParser.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.h +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/test.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/test_list.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/CMakeLists.txt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/__pycache__ -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/SearchDb.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/TestDbCLI.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/moe_like.dsc -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/CreateDb.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.sdf -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Compounds.sqlt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Fingerprints.sqlt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/loadErrors.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/AtomPairs.sqlt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Descriptors.sqlt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/pubchem.200.sdf --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/README +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Compounds.sqlt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/AtomPairs.sqlt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Fingerprints.sqlt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.2.smi --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.smi +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/README +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/pubchem.200.sdf -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr_q1.mol --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.sdf +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.smi +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/SearchDb.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Scripts --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Scripts/test.sh --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Scripts/PythonFormat.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Scripts/README.md -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Scripts/create_deb_packages.sh +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Scripts/test.sh +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Scripts/PythonFormat.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Scripts/FeatFinderCLI.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/README -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/license.txt @@ -34568,12 +34667,12 @@ -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/test.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/ConcurrentQueue.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/hash +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/extensions.hpp -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail/float_functions.hpp -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail/hash_float.hpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/extensions.hpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash_fwd.hpp -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash.hpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash_fwd.hpp -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitRDBoost.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitRDBoost.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitRDBoost.so @@ -35123,12 +35222,12 @@ make[1]: Entering directory '/build/reproducible-path/rdkit-202209.3' dh_python3 -ppython3-rdkit I: dh_python3 fs:483: renaming rdBase.so to rdBase.cpython-311-i386-linux-gnu.so -I: dh_python3 fs:483: renaming DistGeom.so to DistGeom.cpython-311-i386-linux-gnu.so -I: dh_python3 fs:483: renaming rdForceField.so to rdForceField.cpython-311-i386-linux-gnu.so +I: dh_python3 fs:483: renaming Clustering.so to Clustering.cpython-311-i386-linux-gnu.so +I: dh_python3 fs:483: renaming rdInfoTheory.so to rdInfoTheory.cpython-311-i386-linux-gnu.so +I: dh_python3 fs:483: renaming cQuantize.so to cQuantize.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdSimDivPickers.so to rdSimDivPickers.cpython-311-i386-linux-gnu.so -I: dh_python3 fs:483: renaming rdAlignment.so to rdAlignment.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdGeometry.so to rdGeometry.cpython-311-i386-linux-gnu.so -I: dh_python3 fs:483: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-311-i386-linux-gnu.so +I: dh_python3 fs:483: renaming rdAlignment.so to rdAlignment.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdAbbreviations.so to rdAbbreviations.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdCIPLabeler.so to rdCIPLabeler.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdChemReactions.so to rdChemReactions.cpython-311-i386-linux-gnu.so @@ -35165,12 +35264,12 @@ I: dh_python3 fs:483: renaming rdqueries.so to rdqueries.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdtrajectory.so to rdtrajectory.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdMolDraw2D.so to rdMolDraw2D.cpython-311-i386-linux-gnu.so -I: dh_python3 fs:483: renaming rdScaffoldNetwork.so to rdScaffoldNetwork.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdMolStandardize.so to rdMolStandardize.cpython-311-i386-linux-gnu.so +I: dh_python3 fs:483: renaming rdScaffoldNetwork.so to rdScaffoldNetwork.cpython-311-i386-linux-gnu.so +I: dh_python3 fs:483: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-311-i386-linux-gnu.so +I: dh_python3 fs:483: renaming DistGeom.so to DistGeom.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming cDataStructs.so to cDataStructs.cpython-311-i386-linux-gnu.so -I: dh_python3 fs:483: renaming cQuantize.so to cQuantize.cpython-311-i386-linux-gnu.so -I: dh_python3 fs:483: renaming Clustering.so to Clustering.cpython-311-i386-linux-gnu.so -I: dh_python3 fs:483: renaming rdInfoTheory.so to rdInfoTheory.cpython-311-i386-linux-gnu.so +I: dh_python3 fs:483: renaming rdForceField.so to rdForceField.cpython-311-i386-linux-gnu.so dh_numpy3 -ppython3-rdkit make[1]: Leaving directory '/build/reproducible-path/rdkit-202209.3' dh_installsystemduser -O--buildsystem=cmake -O--parallel @@ -35801,33 +35900,33 @@ dh_shlibdeps -a -O--buildsystem=cmake -O--parallel dh_installdeb -O--buildsystem=cmake -O--parallel dh_gencontrol -O--buildsystem=cmake -O--parallel -dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package rdkit-doc: substitution variable ${shlibs:Depends} used, but is not defined -dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined -dpkg-gencontrol: warning: package rdkit-data: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package postgresql-15-rdkit: substitution variable ${postgresql:Depends} unused, but is defined dpkg-gencontrol: warning: package postgresql-15-rdkit: substitution variable ${python3:Depends} unused, but is defined -dpkg-gencontrol: warning: package librdkit-dev: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined +dpkg-gencontrol: warning: package rdkit-data: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package python3-rdkit: substitution variable ${python3:Versions} used, but is not defined -dpkg-gencontrol: warning: package librdkit1: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package rdkit-doc: substitution variable ${python3:Depends} unused, but is defined -dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined +dpkg-gencontrol: warning: package librdkit-dev: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: package librdkit1: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package postgresql-15-rdkit: substitution variable ${postgresql:Depends} unused, but is defined dpkg-gencontrol: warning: package postgresql-15-rdkit: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined dpkg-gencontrol: warning: package python3-rdkit: substitution variable ${python3:Versions} used, but is not defined dpkg-gencontrol: warning: package librdkit1: substitution variable ${python3:Depends} unused, but is defined dh_md5sums -O--buildsystem=cmake -O--parallel dh_builddeb -O--buildsystem=cmake -O--parallel -dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202209.3-1_i386.deb'. -dpkg-deb: building package 'postgresql-15-rdkit-dbgsym' in '../postgresql-15-rdkit-dbgsym_202209.3-1_i386.deb'. +dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202209.3-1_all.deb'. dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202209.3-1_i386.deb'. dpkg-deb: building package 'librdkit1' in '../librdkit1_202209.3-1_i386.deb'. dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202209.3-1_i386.deb'. -dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202209.3-1_all.deb'. +dpkg-deb: building package 'postgresql-15-rdkit-dbgsym' in '../postgresql-15-rdkit-dbgsym_202209.3-1_i386.deb'. +dpkg-deb: building package 'postgresql-15-rdkit' in '../postgresql-15-rdkit_202209.3-1_i386.deb'. dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202209.3-1_all.deb'. +dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202209.3-1_i386.deb'. dpkg-deb: building package 'librdkit1-dbgsym' in '../librdkit1-dbgsym_202209.3-1_i386.deb'. -dpkg-deb: building package 'postgresql-15-rdkit' in '../postgresql-15-rdkit_202209.3-1_i386.deb'. dpkg-genbuildinfo --build=binary -O../rdkit_202209.3-1_i386.buildinfo dpkg-genchanges --build=binary -O../rdkit_202209.3-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -35835,12 +35934,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/8554/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/8554/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/22977 and its subdirectories -I: Current time: Thu Feb 20 19:40:57 -12 2025 -I: pbuilder-time-stamp: 1740123657 +I: removing directory /srv/workspace/pbuilder/8554 and its subdirectories +I: Current time: Sat Jan 20 16:10:07 +14 2024 +I: pbuilder-time-stamp: 1705716607