I: pbuilder: network access will be disabled during build 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 W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [rdkit_202209.3-1.dsc] I: copying [./rdkit_202209.3.orig.tar.xz] I: copying [./rdkit_202209.3-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Jan 14 12:24:43 2023 gpgv: using RSA key 9CA877749FAB2E4FA96862ECDC686A27B43481B0 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./rdkit_202209.3-1.dsc: no acceptable signature found dpkg-source: info: extracting rdkit in rdkit-202209.3 dpkg-source: info: unpacking rdkit_202209.3.orig.tar.xz dpkg-source: info: unpacking rdkit_202209.3-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying NoDownloads.patch dpkg-source: info: applying postgres_Makefile_fixes.patch dpkg-source: info: applying sphinx_imgconverter.patch dpkg-source: info: applying catch2_header.patch dpkg-source: info: applying postgres_alternative_test_outputs.patch dpkg-source: info: applying sphinx_compile_fixes.patch 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/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 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=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 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 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 -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 42920 Sep 20 2022 cat -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp -rwxr-xr-x 1 root root 136916 Jan 5 2023 dash -rwxr-xr-x 1 root root 137160 Sep 20 2022 date -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd -rwxr-xr-x 1 root root 108940 Sep 20 2022 df -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir -rwxr-xr-x 1 root root 87760 Mar 23 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 38760 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 34664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 84272 Mar 23 2023 findmnt -rwsr-xr-x 1 root root 30240 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 218680 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip -rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln -rwxr-xr-x 1 root root 55600 Mar 23 2023 login -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls -rwxr-xr-x 1 root root 214568 Mar 23 2023 lsblk -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 63016 Mar 23 2023 more -rwsr-xr-x 1 root root 58912 Mar 23 2023 mount -rwxr-xr-x 1 root root 13856 Mar 23 2023 mountpoint -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -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 23:46 run-parts -rwxr-xr-x 1 root root 133224 Jan 5 2023 sed 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 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 -rwsr-xr-x 1 root root 30236 Mar 23 2023 umount -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir -rwxr-xr-x 1 root root 71216 Mar 23 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -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/8554/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: bison, catch2, cmake, debhelper-compat (= 13), dh-python, doxygen, flex, imagemagick, latexmk, libboost-dev, libboost-iostreams-dev, libboost-python-dev, libboost-regex-dev, libboost-system-dev, libboost-thread-dev, libcairo-dev, libcoordgen-dev, libeigen3-dev, libfreetype6-dev, libmaeparser-dev, librsvg2-bin, libsqlite3-dev, pandoc, postgresql-server-dev-all, python3-dev, python3-numpy, python3-pandas, python3-pil | python3-imaging, python3-recommonmark, python3-sphinx, python3-sqlalchemy, rapidjson-dev, tex-gyre, texlive-fonts-recommended, texlive-latex-base, texlive-latex-extra, texlive-latex-recommended dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18156 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on bison; however: Package bison is not installed. pbuilder-satisfydepends-dummy depends on catch2; however: Package catch2 is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on flex; however: Package flex is not installed. pbuilder-satisfydepends-dummy depends on imagemagick; however: Package imagemagick is not installed. pbuilder-satisfydepends-dummy depends on latexmk; however: Package latexmk is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-python-dev; however: Package libboost-python-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-regex-dev; however: Package libboost-regex-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-system-dev; however: Package libboost-system-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-thread-dev; however: Package libboost-thread-dev is not installed. pbuilder-satisfydepends-dummy depends on libcairo-dev; however: Package libcairo-dev is not installed. pbuilder-satisfydepends-dummy depends on libcoordgen-dev; however: Package libcoordgen-dev is not installed. pbuilder-satisfydepends-dummy depends on libeigen3-dev; however: Package libeigen3-dev is not installed. pbuilder-satisfydepends-dummy depends on libfreetype6-dev; however: Package libfreetype6-dev is not installed. pbuilder-satisfydepends-dummy depends on libmaeparser-dev; however: Package libmaeparser-dev is not installed. pbuilder-satisfydepends-dummy depends on librsvg2-bin; however: Package librsvg2-bin is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. pbuilder-satisfydepends-dummy depends on pandoc; however: Package pandoc is not installed. pbuilder-satisfydepends-dummy depends on postgresql-server-dev-all; however: Package postgresql-server-dev-all is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-pil | python3-imaging; however: Package python3-pil is not installed. Package python3-imaging is not installed. pbuilder-satisfydepends-dummy depends on python3-recommonmark; however: Package python3-recommonmark is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-sqlalchemy; however: Package python3-sqlalchemy is not installed. pbuilder-satisfydepends-dummy depends on rapidjson-dev; however: Package rapidjson-dev is not installed. pbuilder-satisfydepends-dummy depends on tex-gyre; however: Package tex-gyre is not installed. pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however: Package texlive-fonts-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-base; however: Package texlive-latex-base is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however: Package texlive-latex-extra is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-recommended; however: Package texlive-latex-recommended is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bison{a} bsdextrautils{a} ca-certificates{a} catch2{a} clang-14{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} doxygen{a} dwz{a} file{a} flex{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-lmodern{a} gettext{a} gettext-base{a} groff-base{a} hicolor-icon-theme{a} icu-devtools{a} imagemagick{a} imagemagick-6-common{a} imagemagick-6.q16{a} intltool-debian{a} latexmk{a} libaom3{a} libapache-pom-java{a} libarchive-zip-perl{a} libarchive13{a} libblas3{a} libblkid-dev{a} libboost-atomic1.74-dev{a} libboost-atomic1.74.0{a} libboost-chrono1.74-dev{a} libboost-chrono1.74.0{a} libboost-date-time1.74-dev{a} libboost-date-time1.74.0{a} libboost-dev{a} libboost-iostreams-dev{a} libboost-iostreams1.74-dev{a} libboost-python-dev{a} libboost-python1.74-dev{a} libboost-python1.74.0{a} libboost-regex-dev{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost-serialization1.74-dev{a} libboost-serialization1.74.0{a} libboost-system-dev{a} libboost-system1.74-dev{a} libboost-system1.74.0{a} libboost-thread-dev{a} libboost-thread1.74-dev{a} libboost-thread1.74.0{a} libboost1.74-dev{a} libbrotli-dev{a} libbrotli1{a} libbsd0{a} libcairo-gobject2{a} libcairo-script-interpreter2{a} libcairo2{a} libcairo2-dev{a} libclang-common-14-dev{a} libclang-cpp14{a} libclang1-14{a} libcommons-logging-java{a} libcommons-parent-java{a} libcoordgen-dev{a} libcoordgen3{a} libcurl3-nss{a} libcurl4{a} libdatrie1{a} libdav1d6{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libeigen3-dev{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libffi-dev{a} libfftw3-double3{a} libfile-stripnondeterminism-perl{a} libfontbox-java{a} libfontconfig-dev{a} libfontconfig1{a} libfontenc1{a} libfreetype-dev{a} libfreetype6{a} libfribidi0{a} libgc1{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgfortran5{a} libglib2.0-0{a} libglib2.0-bin{a} libglib2.0-data{a} libglib2.0-dev{a} libglib2.0-dev-bin{a} libgraphite2-3{a} libharfbuzz0b{a} libheif1{a} libice-dev{a} libice6{a} libicu-dev{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libjsoncpp25{a} libkpathsea6{a} liblapack3{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libllvm14{a} liblqr-1-0{a} libltdl7{a} liblua5.3-0{a} liblzo2-2{a} libmaeparser-dev{a} libmaeparser1{a} libmagic-mgc{a} libmagic1{a} libmagickcore-6.q16-6{a} libmagickwand-6.q16-6{a} libmount-dev{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libnspr4{a} libnss3{a} libnuma1{a} libobjc-12-dev{a} libobjc4{a} libopenjp2-7{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpdfbox-java{a} libpfm4{a} libpipeline1{a} libpixman-1-0{a} libpixman-1-dev{a} libpkgconf3{a} libpng-dev{a} libpng16-16{a} libpq-dev{a} libpq5{a} libproc2-0{a} libpsl5{a} libptexenc1{a} libpthread-stubs0-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libraqm0{a} libreadline8{a} librhash0{a} librsvg2-2{a} librsvg2-bin{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libselinux1-dev{a} libsepol-dev{a} libsm-dev{a} libsm6{a} libsqlite3-dev{a} libssh2-1{a} libssl-dev{a} libsub-override-perl{a} libsynctex2{a} libteckit0{a} libtexlua53-5{a} libthai-data{a} libthai0{a} libtiff6{a} libtinfo-dev{a} libtool{a} libuchardet0{a} libuv1{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libx11-dev{a} libx265-199{a} libxau-dev{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-render0-dev{a} libxcb-shm0{a} libxcb-shm0-dev{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxi6{a} libxml2{a} libxml2-dev{a} libxmu6{a} libxpm4{a} libxrender-dev{a} libxrender1{a} libxt6{a} libyaml-0-2{a} libz3-4{a} libz3-dev{a} libzzip-0-13{a} llvm-14{a} llvm-14-dev{a} llvm-14-linker-tools{a} llvm-14-runtime{a} llvm-14-tools{a} m4{a} mailcap{a} man-db{a} media-types{a} mime-support{a} netbase{a} nss-plugin-pem{a} openssl{a} pandoc{a} pandoc-data{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} postgresql-client-15{a} postgresql-client-common{a} postgresql-common{a} postgresql-server-dev-15{a} postgresql-server-dev-all{a} preview-latex-style{a} procps{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-commonmark{a} python3-dateutil{a} python3-dev{a} python3-distutils{a} python3-docutils{a} python3-greenlet{a} python3-idna{a} python3-imagesize{a} python3-jinja2{a} python3-lib2to3{a} python3-markupsafe{a} python3-minimal{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pkg-resources{a} python3-pygments{a} python3-recommonmark{a} python3-requests{a} python3-roman{a} python3-six{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sqlalchemy{a} python3-tz{a} python3-urllib3{a} python3-yaml{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} rapidjson-dev{a} readline-common{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} sphinx-common{a} ssl-cert{a} t1utils{a} tex-common{a} tex-gyre{a} texlive-base{a} texlive-binaries{a} texlive-fonts-recommended{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} tzdata{a} ucf{a} uuid-dev{a} x11-common{a} x11proto-core-dev{a} x11proto-dev{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} xorg-sgml-doctools{a} xtrans-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: apvlv atril binfmt-support curl default-jre dvisvgm e2fsprogs evince fonts-texgyre fonts-texgyre-math ghostscript gsfonts gv javascript-common libarchive-cpio-perl libclang-rt-14-dev libfile-mimeinfo-perl libfl-dev libgdk-pixbuf2.0-bin libgpm2 libjson-xs-perl libldap-common libltdl-dev libmagickcore-6.q16-6-extra libmail-sendmail-perl libnet-dbus-perl libpng-tools librsvg2-common libsasl2-modules libspreadsheet-parseexcel-perl libx11-protocol-perl lmodern logrotate lynx mupdf netpbm okular psmisc publicsuffix python3-bottleneck python3-bs4 python3-html5lib python3-lxml python3-matplotlib python3-numexpr python3-odf python3-olefile python3-openpyxl python3-scipy python3-sqlalchemy-ext python3-tables qpdfview qpdfview-ps-plugin ruby systemd texlive-plain-generic tipa tk viewpdf.app wget x11-utils x11-xserver-utils xdg-user-dirs xpdf zathura-pdf-poppler zathura-ps 0 packages upgraded, 332 newly installed, 0 to remove and 0 not upgraded. Need to get 393 MB of archives. After unpacking 1932 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB] Get: 2 http://deb.debian.org/debian bookworm/main i386 flex i386 2.6.4-8.2 [412 kB] Get: 3 http://deb.debian.org/debian bookworm/main i386 libfftw3-double3 i386 3.3.10-1 [633 kB] Get: 4 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB] Get: 5 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB] Get: 6 http://deb.debian.org/debian bookworm/main i386 libpng16-16 i386 1.6.39-2 [283 kB] Get: 7 http://deb.debian.org/debian bookworm/main i386 libfreetype6 i386 2.12.1+dfsg-5 [410 kB] Get: 8 http://deb.debian.org/debian bookworm/main i386 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 9 http://deb.debian.org/debian bookworm/main i386 fontconfig-config i386 2.14.1-4 [315 kB] Get: 10 http://deb.debian.org/debian bookworm/main i386 libfontconfig1 i386 2.14.1-4 [398 kB] Get: 11 http://deb.debian.org/debian bookworm/main i386 libaom3 i386 3.6.0-1 [1895 kB] Get: 12 http://deb.debian.org/debian bookworm/main i386 libdav1d6 i386 1.0.0-2 [316 kB] Get: 13 http://deb.debian.org/debian bookworm/main i386 libde265-0 i386 1.0.11-1+deb12u1 [193 kB] Get: 14 http://deb.debian.org/debian bookworm/main i386 libnuma1 i386 2.0.16-1 [22.7 kB] Get: 15 http://deb.debian.org/debian bookworm/main i386 libx265-199 i386 3.5-2+b1 [687 kB] Get: 16 http://deb.debian.org/debian bookworm/main i386 libheif1 i386 1.15.1-1 [230 kB] Get: 17 http://deb.debian.org/debian bookworm/main i386 libjbig0 i386 2.1-6.1 [31.6 kB] Get: 18 http://deb.debian.org/debian bookworm/main i386 libjpeg62-turbo i386 1:2.1.5-2 [169 kB] Get: 19 http://deb.debian.org/debian bookworm/main i386 liblcms2-2 i386 2.14-2 [165 kB] Get: 20 http://deb.debian.org/debian bookworm/main i386 libglib2.0-0 i386 2.74.6-2 [1467 kB] Get: 21 http://deb.debian.org/debian bookworm/main i386 liblqr-1-0 i386 0.4.2-2.1 [30.6 kB] Get: 22 http://deb.debian.org/debian bookworm/main i386 libltdl7 i386 2.4.7-5 [394 kB] Get: 23 http://deb.debian.org/debian bookworm/main i386 libopenjp2-7 i386 2.5.0-2 [196 kB] Get: 24 http://deb.debian.org/debian bookworm/main i386 libdeflate0 i386 1.14-1 [57.5 kB] Get: 25 http://deb.debian.org/debian bookworm/main i386 liblerc4 i386 4.0.0+ds-2 [181 kB] Get: 26 http://deb.debian.org/debian bookworm/main i386 libwebp7 i386 1.2.4-0.2+deb12u1 [294 kB] Get: 27 http://deb.debian.org/debian bookworm/main i386 libtiff6 i386 4.5.0-6+deb12u1 [332 kB] Get: 28 http://deb.debian.org/debian bookworm/main i386 libwebpdemux2 i386 1.2.4-0.2+deb12u1 [99.8 kB] Get: 29 http://deb.debian.org/debian bookworm/main i386 libwebpmux3 i386 1.2.4-0.2+deb12u1 [111 kB] Get: 30 http://deb.debian.org/debian bookworm/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 31 http://deb.debian.org/debian bookworm/main i386 libbsd0 i386 0.11.7-2 [121 kB] Get: 32 http://deb.debian.org/debian bookworm/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 33 http://deb.debian.org/debian bookworm/main i386 libxcb1 i386 1.15-1 [148 kB] Get: 34 http://deb.debian.org/debian bookworm/main i386 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get: 35 http://deb.debian.org/debian bookworm/main i386 libx11-6 i386 2:1.8.4-2+deb12u2 [782 kB] Get: 36 http://deb.debian.org/debian bookworm/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 37 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB] Get: 38 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.3~deb12u1 [720 kB] Get: 39 http://deb.debian.org/debian bookworm/main i386 imagemagick-6-common all 8:6.9.11.60+dfsg-1.6 [165 kB] Get: 40 http://deb.debian.org/debian bookworm/main i386 libmagickcore-6.q16-6 i386 8:6.9.11.60+dfsg-1.6 [1843 kB] Get: 41 http://deb.debian.org/debian bookworm/main i386 libmagickwand-6.q16-6 i386 8:6.9.11.60+dfsg-1.6 [389 kB] Get: 42 http://deb.debian.org/debian bookworm/main i386 libjson-perl all 4.10000-1 [87.5 kB] Get: 43 http://deb.debian.org/debian bookworm/main i386 netbase all 6.4 [12.8 kB] Get: 44 http://deb.debian.org/debian bookworm/main i386 postgresql-client-common all 248 [35.1 kB] Get: 45 http://deb.debian.org/debian bookworm/main i386 openssl i386 3.0.11-1~deb12u2 [1423 kB] Get: 46 http://deb.debian.org/debian bookworm/main i386 ssl-cert all 1.1.2 [21.1 kB] Get: 47 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 48 http://deb.debian.org/debian bookworm/main i386 ucf all 3.0043+nmu1 [55.2 kB] Get: 49 http://deb.debian.org/debian bookworm/main i386 postgresql-common all 248 [179 kB] Get: 50 http://deb.debian.org/debian bookworm/main i386 libpython3.11-minimal i386 3.11.2-6 [813 kB] Get: 51 http://deb.debian.org/debian bookworm/main i386 python3.11-minimal i386 3.11.2-6 [2130 kB] Get: 52 http://deb.debian.org/debian bookworm/main i386 python3-minimal i386 3.11.2-1+b1 [26.3 kB] Get: 53 http://deb.debian.org/debian bookworm/main i386 media-types all 10.0.0 [26.1 kB] Get: 54 http://deb.debian.org/debian bookworm/main i386 mailcap all 3.70+nmu1 [32.0 kB] Get: 55 http://deb.debian.org/debian bookworm/main i386 mime-support all 3.66 [10.9 kB] Get: 56 http://deb.debian.org/debian bookworm/main i386 readline-common all 8.2-1.3 [69.0 kB] Get: 57 http://deb.debian.org/debian bookworm/main i386 libreadline8 i386 8.2-1.3 [171 kB] Get: 58 http://deb.debian.org/debian bookworm/main i386 libpython3.11-stdlib i386 3.11.2-6 [1799 kB] Get: 59 http://deb.debian.org/debian bookworm/main i386 python3.11 i386 3.11.2-6 [572 kB] Get: 60 http://deb.debian.org/debian bookworm/main i386 libpython3-stdlib i386 3.11.2-1+b1 [9308 B] Get: 61 http://deb.debian.org/debian bookworm/main i386 python3 i386 3.11.2-1+b1 [26.3 kB] Get: 62 http://deb.debian.org/debian bookworm/main i386 sgml-base all 1.31 [15.4 kB] Get: 63 http://deb.debian.org/debian bookworm/main i386 tzdata all 2023c-5+deb12u1 [296 kB] Get: 64 http://deb.debian.org/debian bookworm/main i386 libproc2-0 i386 2:4.0.2-3 [63.7 kB] Get: 65 http://deb.debian.org/debian bookworm/main i386 procps i386 2:4.0.2-3 [706 kB] Get: 66 http://deb.debian.org/debian bookworm/main i386 ca-certificates all 20230311 [153 kB] Get: 67 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB] Get: 68 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB] Get: 69 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB] Get: 70 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB] Get: 71 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 72 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB] Get: 73 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB] Get: 74 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB] Get: 75 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB] Get: 76 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB] Get: 77 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 78 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 79 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB] Get: 80 http://deb.debian.org/debian bookworm/main i386 bison i386 2:3.8.2+dfsg-1+b1 [1186 kB] Get: 81 http://deb.debian.org/debian bookworm/main i386 catch2 i386 2.13.10-1 [483 kB] Get: 82 http://deb.debian.org/debian bookworm/main i386 libedit2 i386 3.1-20221030-2 [97.2 kB] Get: 83 http://deb.debian.org/debian bookworm/main i386 libz3-4 i386 4.8.12-3.1 [7853 kB] Get: 84 http://deb.debian.org/debian bookworm/main i386 libllvm14 i386 1:14.0.6-12 [25.0 MB] Get: 85 http://deb.debian.org/debian bookworm/main i386 libclang-cpp14 i386 1:14.0.6-12 [12.7 MB] Get: 86 http://deb.debian.org/debian bookworm/main i386 libgc1 i386 1:8.2.2-3 [246 kB] Get: 87 http://deb.debian.org/debian bookworm/main i386 libobjc4 i386 12.2.0-14 [45.6 kB] Get: 88 http://deb.debian.org/debian bookworm/main i386 libobjc-12-dev i386 12.2.0-14 [165 kB] Get: 89 http://deb.debian.org/debian bookworm/main i386 libclang-common-14-dev all 1:14.0.6-12 [890 kB] Get: 90 http://deb.debian.org/debian bookworm/main i386 llvm-14-linker-tools i386 1:14.0.6-12 [1383 kB] Get: 91 http://deb.debian.org/debian bookworm/main i386 libclang1-14 i386 1:14.0.6-12 [7086 kB] Get: 92 http://deb.debian.org/debian bookworm/main i386 clang-14 i386 1:14.0.6-12 [106 kB] Get: 93 http://deb.debian.org/debian bookworm/main i386 libarchive13 i386 3.6.2-1 [385 kB] Get: 94 http://deb.debian.org/debian bookworm/main i386 libsasl2-modules-db i386 2.1.28+dfsg-10 [21.4 kB] Get: 95 http://deb.debian.org/debian bookworm/main i386 libsasl2-2 i386 2.1.28+dfsg-10 [62.7 kB] Get: 96 http://deb.debian.org/debian bookworm/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5 [196 kB] Get: 97 http://deb.debian.org/debian bookworm/main i386 libnghttp2-14 i386 1.52.0-1+deb12u1 [80.7 kB] Get: 98 http://deb.debian.org/debian bookworm/main i386 libpsl5 i386 0.21.2-1 [59.3 kB] Get: 99 http://deb.debian.org/debian bookworm/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 100 http://deb.debian.org/debian bookworm/main i386 libssh2-1 i386 1.10.0-3+b1 [187 kB] Get: 101 http://deb.debian.org/debian bookworm/main i386 libcurl4 i386 7.88.1-10+deb12u4 [424 kB] Get: 102 http://deb.debian.org/debian bookworm/main i386 libjsoncpp25 i386 1.9.5-4 [86.2 kB] Get: 103 http://deb.debian.org/debian bookworm/main i386 librhash0 i386 1.4.3-3 [149 kB] Get: 104 http://deb.debian.org/debian bookworm/main i386 libuv1 i386 1.44.2-1 [147 kB] Get: 105 http://deb.debian.org/debian bookworm/main i386 cmake-data all 3.25.1-1 [2026 kB] Get: 106 http://deb.debian.org/debian bookworm/main i386 cmake i386 3.25.1-1 [9767 kB] Get: 107 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 108 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB] Get: 109 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB] Get: 110 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 111 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B] Get: 112 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 113 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 114 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB] Get: 115 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB] Get: 116 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB] Get: 117 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 118 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 119 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB] Get: 120 http://deb.debian.org/debian bookworm/main i386 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 121 http://deb.debian.org/debian bookworm/main i386 python3-distutils all 3.11.2-3 [131 kB] Get: 122 http://deb.debian.org/debian bookworm/main i386 dh-python all 5.20230130+deb12u1 [104 kB] Get: 123 http://deb.debian.org/debian bookworm/main i386 xml-core all 0.18+nmu1 [23.8 kB] Get: 124 http://deb.debian.org/debian bookworm/main i386 docutils-common all 0.19+dfsg-6 [127 kB] Get: 125 http://deb.debian.org/debian bookworm/main i386 doxygen i386 1.9.4-4 [4836 kB] Get: 126 http://deb.debian.org/debian bookworm/main i386 fontconfig i386 2.14.1-4 [450 kB] Get: 127 http://deb.debian.org/debian bookworm/main i386 fonts-lmodern all 2.005-1 [4540 kB] Get: 128 http://deb.debian.org/debian bookworm/main i386 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 129 http://deb.debian.org/debian bookworm/main i386 icu-devtools i386 72.1-3 [214 kB] Get: 130 http://deb.debian.org/debian bookworm/main i386 imagemagick-6.q16 i386 8:6.9.11.60+dfsg-1.6 [339 kB] Get: 131 http://deb.debian.org/debian bookworm/main i386 imagemagick i386 8:6.9.11.60+dfsg-1.6 [122 kB] Get: 132 http://deb.debian.org/debian bookworm/main i386 tex-common all 6.18 [32.5 kB] Get: 133 http://deb.debian.org/debian bookworm/main i386 libpaper1 i386 1.1.29 [12.7 kB] Get: 134 http://deb.debian.org/debian bookworm/main i386 libpaper-utils i386 1.1.29 [8972 B] Get: 135 http://deb.debian.org/debian bookworm/main i386 libkpathsea6 i386 2022.20220321.62855-5.1+deb12u1 [155 kB] Get: 136 http://deb.debian.org/debian bookworm/main i386 libptexenc1 i386 2022.20220321.62855-5.1+deb12u1 [44.8 kB] Get: 137 http://deb.debian.org/debian bookworm/main i386 libsynctex2 i386 2022.20220321.62855-5.1+deb12u1 [62.5 kB] Get: 138 http://deb.debian.org/debian bookworm/main i386 libtexlua53-5 i386 2022.20220321.62855-5.1+deb12u1 [126 kB] Get: 139 http://deb.debian.org/debian bookworm/main i386 t1utils i386 1.41-4 [62.3 kB] Get: 140 http://deb.debian.org/debian bookworm/main i386 libpixman-1-0 i386 0.42.2-1 [548 kB] Get: 141 http://deb.debian.org/debian bookworm/main i386 libxcb-render0 i386 1.15-1 [116 kB] Get: 142 http://deb.debian.org/debian bookworm/main i386 libxcb-shm0 i386 1.15-1 [106 kB] Get: 143 http://deb.debian.org/debian bookworm/main i386 libxrender1 i386 1:0.9.10-1.1 [34.1 kB] Get: 144 http://deb.debian.org/debian bookworm/main i386 libcairo2 i386 1.16.0-7 [627 kB] Get: 145 http://deb.debian.org/debian bookworm/main i386 libgraphite2-3 i386 1.3.14-1 [84.0 kB] Get: 146 http://deb.debian.org/debian bookworm/main i386 libharfbuzz0b i386 6.0.0+dfsg-3 [1966 kB] Get: 147 http://deb.debian.org/debian bookworm/main i386 libteckit0 i386 2.5.11+ds1-1+b1 [282 kB] Get: 148 http://deb.debian.org/debian bookworm/main i386 x11-common all 1:7.7+23 [252 kB] Get: 149 http://deb.debian.org/debian bookworm/main i386 libice6 i386 2:1.0.10-1 [60.8 kB] Get: 150 http://deb.debian.org/debian bookworm/main i386 libsm6 i386 2:1.2.3-1 [35.7 kB] Get: 151 http://deb.debian.org/debian bookworm/main i386 libxt6 i386 1:1.2.1-1.1 [192 kB] Get: 152 http://deb.debian.org/debian bookworm/main i386 libxmu6 i386 2:1.1.3-3 [62.5 kB] Get: 153 http://deb.debian.org/debian bookworm/main i386 libxpm4 i386 1:3.5.12-1.1+deb12u1 [50.4 kB] Get: 154 http://deb.debian.org/debian bookworm/main i386 libxaw7 i386 2:1.0.14-1 [209 kB] Get: 155 http://deb.debian.org/debian bookworm/main i386 libxi6 i386 2:1.8-1+b1 [86.2 kB] Get: 156 http://deb.debian.org/debian bookworm/main i386 libzzip-0-13 i386 0.13.72+dfsg.1-1.1 [60.1 kB] Get: 157 http://deb.debian.org/debian bookworm/main i386 texlive-binaries i386 2022.20220321.62855-5.1+deb12u1 [8537 kB] Get: 158 http://deb.debian.org/debian bookworm/main i386 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 159 http://deb.debian.org/debian bookworm/main i386 texlive-base all 2022.20230122-3 [21.9 MB] Get: 160 http://deb.debian.org/debian bookworm/main i386 texlive-latex-base all 2022.20230122-3 [1182 kB] Get: 161 http://deb.debian.org/debian bookworm/main i386 latexmk all 1:4.79-1 [198 kB] Get: 162 http://deb.debian.org/debian bookworm/main i386 libapache-pom-java all 29-2 [5276 B] Get: 163 http://deb.debian.org/debian bookworm/main i386 libblas3 i386 3.11.0-2 [139 kB] Get: 164 http://deb.debian.org/debian bookworm/main i386 uuid-dev i386 2.38.1-5+b1 [40.2 kB] Get: 165 http://deb.debian.org/debian bookworm/main i386 libblkid-dev i386 2.38.1-5+b1 [202 kB] Get: 166 http://deb.debian.org/debian bookworm/main i386 libboost1.74-dev i386 1.74.0+ds1-21 [9508 kB] Get: 167 http://deb.debian.org/debian bookworm/main i386 libboost-atomic1.74.0 i386 1.74.0+ds1-21 [221 kB] Get: 168 http://deb.debian.org/debian bookworm/main i386 libboost-atomic1.74-dev i386 1.74.0+ds1-21 [222 kB] Get: 169 http://deb.debian.org/debian bookworm/main i386 libboost-chrono1.74.0 i386 1.74.0+ds1-21 [230 kB] Get: 170 http://deb.debian.org/debian bookworm/main i386 libboost-chrono1.74-dev i386 1.74.0+ds1-21 [237 kB] Get: 171 http://deb.debian.org/debian bookworm/main i386 libboost-date-time1.74.0 i386 1.74.0+ds1-21 [218 kB] Get: 172 http://deb.debian.org/debian bookworm/main i386 libboost-serialization1.74.0 i386 1.74.0+ds1-21 [325 kB] Get: 173 http://deb.debian.org/debian bookworm/main i386 libboost-serialization1.74-dev i386 1.74.0+ds1-21 [368 kB] Get: 174 http://deb.debian.org/debian bookworm/main i386 libboost-date-time1.74-dev i386 1.74.0+ds1-21 [226 kB] Get: 175 http://deb.debian.org/debian bookworm/main i386 libboost-dev i386 1.74.0.3 [4548 B] Get: 176 http://deb.debian.org/debian bookworm/main i386 libboost-regex1.74.0 i386 1.74.0+ds1-21 [509 kB] Get: 177 http://deb.debian.org/debian bookworm/main i386 libicu-dev i386 72.1-3 [10.6 MB] Get: 178 http://deb.debian.org/debian bookworm/main i386 libboost-regex1.74-dev i386 1.74.0+ds1-21 [585 kB] Get: 179 http://deb.debian.org/debian bookworm/main i386 libboost-iostreams1.74-dev i386 1.74.0+ds1-21 [250 kB] Get: 180 http://deb.debian.org/debian bookworm/main i386 libboost-iostreams-dev i386 1.74.0.3 [4320 B] Get: 181 http://deb.debian.org/debian bookworm/main i386 libboost-python1.74.0 i386 1.74.0+ds1-21 [295 kB] Get: 182 http://deb.debian.org/debian bookworm/main i386 libpython3.11 i386 3.11.2-6 [2013 kB] Get: 183 http://deb.debian.org/debian bookworm/main i386 libexpat1-dev i386 2.5.0-1 [158 kB] Get: 184 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB] Get: 185 http://deb.debian.org/debian bookworm/main i386 libpython3.11-dev i386 3.11.2-6 [4906 kB] Get: 186 http://deb.debian.org/debian bookworm/main i386 libpython3-dev i386 3.11.2-1+b1 [9580 B] Get: 187 http://deb.debian.org/debian bookworm/main i386 python3.11-dev i386 3.11.2-6 [615 kB] Get: 188 http://deb.debian.org/debian bookworm/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 189 http://deb.debian.org/debian bookworm/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 190 http://deb.debian.org/debian bookworm/main i386 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 191 http://deb.debian.org/debian bookworm/main i386 python3-dev i386 3.11.2-1+b1 [26.2 kB] Get: 192 http://deb.debian.org/debian bookworm/main i386 libboost-python1.74-dev i386 1.74.0+ds1-21 [319 kB] Get: 193 http://deb.debian.org/debian bookworm/main i386 libboost-python-dev i386 1.74.0.3 [4632 B] Get: 194 http://deb.debian.org/debian bookworm/main i386 libboost-regex-dev i386 1.74.0.3 [4596 B] Get: 195 http://deb.debian.org/debian bookworm/main i386 libboost-system1.74.0 i386 1.74.0+ds1-21 [218 kB] Get: 196 http://deb.debian.org/debian bookworm/main i386 libboost-system1.74-dev i386 1.74.0+ds1-21 [219 kB] Get: 197 http://deb.debian.org/debian bookworm/main i386 libboost-system-dev i386 1.74.0.3 [4472 B] Get: 198 http://deb.debian.org/debian bookworm/main i386 libboost-thread1.74.0 i386 1.74.0+ds1-21 [259 kB] Get: 199 http://deb.debian.org/debian bookworm/main i386 libboost-thread1.74-dev i386 1.74.0+ds1-21 [270 kB] Get: 200 http://deb.debian.org/debian bookworm/main i386 libboost-thread-dev i386 1.74.0.3 [4356 B] Get: 201 http://deb.debian.org/debian bookworm/main i386 libbrotli-dev i386 1.0.9-2+b6 [287 kB] Get: 202 http://deb.debian.org/debian bookworm/main i386 libcairo-gobject2 i386 1.16.0-7 [111 kB] Get: 203 http://deb.debian.org/debian bookworm/main i386 liblzo2-2 i386 2.10-2 [59.7 kB] Get: 204 http://deb.debian.org/debian bookworm/main i386 libcairo-script-interpreter2 i386 1.16.0-7 [153 kB] Get: 205 http://deb.debian.org/debian bookworm/main i386 libpng-dev i386 1.6.39-2 [367 kB] Get: 206 http://deb.debian.org/debian bookworm/main i386 libfreetype-dev i386 2.12.1+dfsg-5 [585 kB] Get: 207 http://deb.debian.org/debian bookworm/main i386 libpkgconf3 i386 1.8.1-1 [38.3 kB] Get: 208 http://deb.debian.org/debian bookworm/main i386 pkgconf-bin i386 1.8.1-1 [29.8 kB] Get: 209 http://deb.debian.org/debian bookworm/main i386 pkgconf i386 1.8.1-1 [25.9 kB] Get: 210 http://deb.debian.org/debian bookworm/main i386 pkg-config i386 1.8.1-1 [13.7 kB] Get: 211 http://deb.debian.org/debian bookworm/main i386 libfontconfig-dev i386 2.14.1-4 [425 kB] Get: 212 http://deb.debian.org/debian bookworm/main i386 libffi-dev i386 3.4.4-1 [57.3 kB] Get: 213 http://deb.debian.org/debian bookworm/main i386 libglib2.0-data all 2.74.6-2 [1207 kB] Get: 214 http://deb.debian.org/debian bookworm/main i386 libglib2.0-bin i386 2.74.6-2 [113 kB] Get: 215 http://deb.debian.org/debian bookworm/main i386 libglib2.0-dev-bin i386 2.74.6-2 [151 kB] Get: 216 http://deb.debian.org/debian bookworm/main i386 libsepol-dev i386 3.4-2.1 [385 kB] Get: 217 http://deb.debian.org/debian bookworm/main i386 libpcre2-16-0 i386 10.42-1 [243 kB] Get: 218 http://deb.debian.org/debian bookworm/main i386 libpcre2-32-0 i386 10.42-1 [232 kB] Get: 219 http://deb.debian.org/debian bookworm/main i386 libpcre2-posix3 i386 10.42-1 [55.4 kB] Get: 220 http://deb.debian.org/debian bookworm/main i386 libpcre2-dev i386 10.42-1 [761 kB] Get: 221 http://deb.debian.org/debian bookworm/main i386 libselinux1-dev i386 3.4-1+b6 [165 kB] Get: 222 http://deb.debian.org/debian bookworm/main i386 libmount-dev i386 2.38.1-5+b1 [22.5 kB] Get: 223 http://deb.debian.org/debian bookworm/main i386 libglib2.0-dev i386 2.74.6-2 [1718 kB] Get: 224 http://deb.debian.org/debian bookworm/main i386 libpixman-1-dev i386 0.42.2-1 [573 kB] Get: 225 http://deb.debian.org/debian bookworm/main i386 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 226 http://deb.debian.org/debian bookworm/main i386 x11proto-dev all 2022.1-1 [599 kB] Get: 227 http://deb.debian.org/debian bookworm/main i386 x11proto-core-dev all 2022.1-1 [3528 B] Get: 228 http://deb.debian.org/debian bookworm/main i386 libice-dev i386 2:1.0.10-1 [70.5 kB] Get: 229 http://deb.debian.org/debian bookworm/main i386 libsm-dev i386 2:1.2.3-1 [38.8 kB] Get: 230 http://deb.debian.org/debian bookworm/main i386 libxau-dev i386 1:1.0.9-1 [23.3 kB] Get: 231 http://deb.debian.org/debian bookworm/main i386 libxdmcp-dev i386 1:1.1.2-3 [42.7 kB] Get: 232 http://deb.debian.org/debian bookworm/main i386 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 233 http://deb.debian.org/debian bookworm/main i386 libpthread-stubs0-dev i386 0.4-1 [5340 B] Get: 234 http://deb.debian.org/debian bookworm/main i386 libxcb1-dev i386 1.15-1 [185 kB] Get: 235 http://deb.debian.org/debian bookworm/main i386 libx11-dev i386 2:1.8.4-2+deb12u2 [864 kB] Get: 236 http://deb.debian.org/debian bookworm/main i386 libxcb-render0-dev i386 1.15-1 [119 kB] Get: 237 http://deb.debian.org/debian bookworm/main i386 libxcb-shm0-dev i386 1.15-1 [107 kB] Get: 238 http://deb.debian.org/debian bookworm/main i386 libxext-dev i386 2:1.3.4-1+b1 [110 kB] Get: 239 http://deb.debian.org/debian bookworm/main i386 libxrender-dev i386 1:0.9.10-1.1 [42.3 kB] Get: 240 http://deb.debian.org/debian bookworm/main i386 libcairo2-dev i386 1.16.0-7 [800 kB] Get: 241 http://deb.debian.org/debian bookworm/main i386 libcommons-parent-java all 56-1 [10.8 kB] Get: 242 http://deb.debian.org/debian bookworm/main i386 libcommons-logging-java all 1.2-3 [62.4 kB] Get: 243 http://deb.debian.org/debian bookworm/main i386 libcoordgen3 i386 3.0.1-1 [220 kB] Get: 244 http://deb.debian.org/debian bookworm/main i386 libcoordgen-dev i386 3.0.1-1 [46.6 kB] Get: 245 http://deb.debian.org/debian bookworm/main i386 libnspr4 i386 2:4.35-1 [123 kB] Get: 246 http://deb.debian.org/debian bookworm/main i386 libnss3 i386 2:3.87.1-1 [1439 kB] Get: 247 http://deb.debian.org/debian bookworm/main i386 nss-plugin-pem i386 1.0.8+1-1 [58.3 kB] Get: 248 http://deb.debian.org/debian bookworm/main i386 libcurl3-nss i386 7.88.1-10+deb12u4 [425 kB] Get: 249 http://deb.debian.org/debian bookworm/main i386 libdatrie1 i386 0.2.13-2+b1 [45.0 kB] Get: 250 http://deb.debian.org/debian bookworm/main i386 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 251 http://deb.debian.org/debian bookworm/main i386 libfontbox-java all 1:1.8.16-2 [211 kB] Get: 252 http://deb.debian.org/debian bookworm/main i386 libfontenc1 i386 1:1.1.4-1 [24.5 kB] Get: 253 http://deb.debian.org/debian bookworm/main i386 libfribidi0 i386 1.0.8-2.1 [65.6 kB] Get: 254 http://deb.debian.org/debian bookworm/main i386 libgdk-pixbuf2.0-common all 2.42.10+dfsg-1 [306 kB] Get: 255 http://deb.debian.org/debian bookworm/main i386 shared-mime-info i386 2.2-1 [730 kB] Get: 256 http://deb.debian.org/debian bookworm/main i386 libgdk-pixbuf-2.0-0 i386 2.42.10+dfsg-1+b1 [147 kB] Get: 257 http://deb.debian.org/debian bookworm/main i386 libgfortran5 i386 12.2.0-14 [698 kB] Get: 258 http://deb.debian.org/debian bookworm/main i386 libimagequant0 i386 2.17.0-1 [32.9 kB] Get: 259 http://deb.debian.org/debian bookworm/main i386 liblapack3 i386 3.11.0-2 [2092 kB] Get: 260 http://deb.debian.org/debian bookworm/main i386 liblua5.3-0 i386 5.3.6-2 [144 kB] Get: 261 http://deb.debian.org/debian bookworm/main i386 libmaeparser1 i386 1.3.0-1 [97.1 kB] Get: 262 http://deb.debian.org/debian bookworm/main i386 libmaeparser-dev i386 1.3.0-1 [13.4 kB] Get: 263 http://deb.debian.org/debian bookworm/main i386 libncurses6 i386 6.4-4 [111 kB] Get: 264 http://deb.debian.org/debian bookworm/main i386 libncurses-dev i386 6.4-4 [379 kB] Get: 265 http://deb.debian.org/debian bookworm/main i386 libthai-data all 0.1.29-1 [176 kB] Get: 266 http://deb.debian.org/debian bookworm/main i386 libthai0 i386 0.1.29-1 [58.6 kB] Get: 267 http://deb.debian.org/debian bookworm/main i386 libpango-1.0-0 i386 1.50.12+ds-1 [220 kB] Get: 268 http://deb.debian.org/debian bookworm/main i386 libpangoft2-1.0-0 i386 1.50.12+ds-1 [50.5 kB] Get: 269 http://deb.debian.org/debian bookworm/main i386 libpangocairo-1.0-0 i386 1.50.12+ds-1 [35.4 kB] Get: 270 http://deb.debian.org/debian bookworm/main i386 libpdfbox-java all 1:1.8.16-2 [5205 kB] Get: 271 http://deb.debian.org/debian bookworm/main i386 libpfm4 i386 4.13.0-1 [241 kB] Get: 272 http://deb.debian.org/debian bookworm/main i386 libpq5 i386 15.5-0+deb12u1 [194 kB] Get: 273 http://deb.debian.org/debian bookworm/main i386 libssl-dev i386 3.0.11-1~deb12u2 [2489 kB] Get: 274 http://deb.debian.org/debian bookworm/main i386 libpq-dev i386 15.5-0+deb12u1 [151 kB] Get: 275 http://deb.debian.org/debian bookworm/main i386 libraqm0 i386 0.7.0-4.1 [11.1 kB] Get: 276 http://deb.debian.org/debian bookworm/main i386 librsvg2-2 i386 2.54.7+dfsg-1~deb12u1 [2750 kB] Get: 277 http://deb.debian.org/debian bookworm/main i386 librsvg2-bin i386 2.54.7+dfsg-1~deb12u1 [1626 kB] Get: 278 http://deb.debian.org/debian bookworm/main i386 libsqlite3-dev i386 3.40.1-2 [1105 kB] Get: 279 http://deb.debian.org/debian bookworm/main i386 libtinfo-dev i386 6.4-4 [924 B] Get: 280 http://deb.debian.org/debian bookworm/main i386 libxml2-dev i386 2.9.14+dfsg-1.3~deb12u1 [846 kB] Get: 281 http://deb.debian.org/debian bookworm/main i386 libyaml-0-2 i386 0.2.5-1 [55.9 kB] Get: 282 http://deb.debian.org/debian bookworm/main i386 libz3-dev i386 4.8.12-3.1 [90.6 kB] Get: 283 http://deb.debian.org/debian bookworm/main i386 llvm-14-runtime i386 1:14.0.6-12 [535 kB] Get: 284 http://deb.debian.org/debian bookworm/main i386 llvm-14 i386 1:14.0.6-12 [13.9 MB] Get: 285 http://deb.debian.org/debian bookworm/main i386 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 286 http://deb.debian.org/debian bookworm/main i386 python3-pygments all 2.14.0+dfsg-1 [783 kB] Get: 287 http://deb.debian.org/debian bookworm/main i386 python3-yaml i386 6.0-3+b2 [119 kB] Get: 288 http://deb.debian.org/debian bookworm/main i386 llvm-14-tools i386 1:14.0.6-12 [435 kB] Get: 289 http://deb.debian.org/debian bookworm/main i386 llvm-14-dev i386 1:14.0.6-12 [36.8 MB] Get: 290 http://deb.debian.org/debian bookworm/main i386 pandoc-data all 2.17.1.1-2~deb12u1 [418 kB] Get: 291 http://deb.debian.org/debian bookworm/main i386 pandoc i386 2.17.1.1-2~deb12u1 [27.7 MB] Get: 292 http://deb.debian.org/debian bookworm/main i386 postgresql-client-15 i386 15.5-0+deb12u1 [1721 kB] Get: 293 http://deb.debian.org/debian bookworm/main i386 postgresql-server-dev-15 i386 15.5-0+deb12u1 [1154 kB] Get: 294 http://deb.debian.org/debian bookworm/main i386 postgresql-server-dev-all i386 248 [20.4 kB] Get: 295 http://deb.debian.org/debian bookworm/main i386 preview-latex-style all 12.2-1 [201 kB] Get: 296 http://deb.debian.org/debian bookworm/main i386 python-babel-localedata all 2.10.3-1 [5615 kB] Get: 297 http://deb.debian.org/debian bookworm/main i386 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 298 http://deb.debian.org/debian bookworm/main i386 python3-tz all 2022.7.1-4 [30.1 kB] Get: 299 http://deb.debian.org/debian bookworm/main i386 python3-babel all 2.10.3-1 [103 kB] Get: 300 http://deb.debian.org/debian bookworm/main i386 python3-certifi all 2022.9.24-1 [153 kB] Get: 301 http://deb.debian.org/debian bookworm/main i386 python3-chardet all 5.1.0+dfsg-2 [110 kB] Get: 302 http://deb.debian.org/debian bookworm/main i386 python3-charset-normalizer all 3.0.1-2 [49.3 kB] Get: 303 http://deb.debian.org/debian bookworm/main i386 python3-commonmark all 0.9.1-4 [45.1 kB] Get: 304 http://deb.debian.org/debian bookworm/main i386 python3-six all 1.16.0-4 [17.5 kB] Get: 305 http://deb.debian.org/debian bookworm/main i386 python3-dateutil all 2.8.2-2 [78.3 kB] Get: 306 http://deb.debian.org/debian bookworm/main i386 python3-roman all 3.3-3 [9880 B] Get: 307 http://deb.debian.org/debian bookworm/main i386 python3-docutils all 0.19+dfsg-6 [382 kB] Get: 308 http://deb.debian.org/debian bookworm/main i386 python3-greenlet i386 2.0.2-1 [146 kB] Get: 309 http://deb.debian.org/debian bookworm/main i386 python3-idna all 3.3-1 [39.4 kB] Get: 310 http://deb.debian.org/debian bookworm/main i386 python3-imagesize all 1.4.1-1 [6688 B] Get: 311 http://deb.debian.org/debian bookworm/main i386 python3-markupsafe i386 2.1.2-1+b1 [13.3 kB] Get: 312 http://deb.debian.org/debian bookworm/main i386 python3-jinja2 all 3.1.2-1 [119 kB] Get: 313 http://deb.debian.org/debian bookworm/main i386 python3-numpy i386 1:1.24.2-1 [6115 kB] Get: 314 http://deb.debian.org/debian bookworm/main i386 python3-packaging all 23.0-1 [32.5 kB] Get: 315 http://deb.debian.org/debian bookworm/main i386 python3-pandas-lib i386 1.5.3+dfsg-2 [3382 kB] Get: 316 http://deb.debian.org/debian bookworm/main i386 python3-pandas all 1.5.3+dfsg-2 [2885 kB] Get: 317 http://deb.debian.org/debian bookworm/main i386 python3-pil i386 9.4.0-1.1+b1 [473 kB] Get: 318 http://deb.debian.org/debian bookworm/main i386 sphinx-common all 5.3.0-4 [653 kB] Get: 319 http://deb.debian.org/debian bookworm/main i386 python3-urllib3 all 1.26.12-1 [117 kB] Get: 320 http://deb.debian.org/debian bookworm/main i386 python3-requests all 2.28.1+dfsg-1 [67.9 kB] Get: 321 http://deb.debian.org/debian bookworm/main i386 python3-snowballstemmer all 2.2.0-2 [57.8 kB] Get: 322 http://deb.debian.org/debian bookworm/main i386 python3-sphinx all 5.3.0-4 [549 kB] Get: 323 http://deb.debian.org/debian bookworm/main i386 python3-recommonmark all 0.7.1+ds-5 [17.3 kB] Get: 324 http://deb.debian.org/debian bookworm/main i386 python3-sqlalchemy all 1.4.46+ds1-1 [1008 kB] Get: 325 http://deb.debian.org/debian bookworm/main i386 rapidjson-dev all 1.1.0+dfsg2-7.1 [97.7 kB] Get: 326 http://deb.debian.org/debian bookworm/main i386 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 327 http://deb.debian.org/debian bookworm/main i386 xfonts-utils i386 1:7.7+6 [95.2 kB] Get: 328 http://deb.debian.org/debian bookworm/main i386 tex-gyre all 20180621-6 [6209 kB] Get: 329 http://deb.debian.org/debian bookworm/main i386 texlive-fonts-recommended all 2022.20230122-3 [4988 kB] 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 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.) Preparing to unpack .../00-m4_1.4.19-3_i386.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package flex. Preparing to unpack .../01-flex_2.6.4-8.2_i386.deb ... Unpacking flex (2.6.4-8.2) ... Selecting previously unselected package libfftw3-double3:i386. Preparing to unpack .../02-libfftw3-double3_3.3.10-1_i386.deb ... Unpacking libfftw3-double3:i386 (3.3.10-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../03-libexpat1_2.5.0-1_i386.deb ... Unpacking libexpat1:i386 (2.5.0-1) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../04-libbrotli1_1.0.9-2+b6_i386.deb ... Unpacking libbrotli1:i386 (1.0.9-2+b6) ... Selecting previously unselected package libpng16-16:i386. Preparing to unpack .../05-libpng16-16_1.6.39-2_i386.deb ... Unpacking libpng16-16:i386 (1.6.39-2) ... Selecting previously unselected package libfreetype6:i386. Preparing to unpack .../06-libfreetype6_2.12.1+dfsg-5_i386.deb ... Unpacking libfreetype6:i386 (2.12.1+dfsg-5) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../07-fonts-dejavu-core_2.37-6_all.deb ... Unpacking fonts-dejavu-core (2.37-6) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../08-fontconfig-config_2.14.1-4_i386.deb ... 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Setting up libcairo2:i386 (1.16.0-7) ... Setting up libfreetype-dev:i386 (2.12.1+dfsg-5) ... Setting up libboost-iostreams1.74-dev:i386 (1.74.0+ds1-21) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libboost-date-time1.74-dev:i386 (1.74.0+ds1-21) ... Setting up libxcb-shm0-dev:i386 (1.15-1) ... Setting up libmagickcore-6.q16-6:i386 (8:6.9.11.60+dfsg-1.6) ... Setting up llvm-14-runtime (1:14.0.6-12) ... Setting up libraqm0:i386 (0.7.0-4.1) ... Setting up sphinx-common (5.3.0-4) ... Setting up postgresql-common (248) ... Creating config file /etc/postgresql-common/createcluster.conf with new version Building PostgreSQL dictionaries from installed myspell/hunspell packages... Removing obsolete dictionary files: invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libclang-common-14-dev (1:14.0.6-12) ... Setting up libclang-cpp14 (1:14.0.6-12) ... 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Setting up libfontconfig-dev:i386 (2.14.1-4) ... Setting up preview-latex-style (12.2-1) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up libxaw7:i386 (2:1.0.14-1) ... Setting up libboost-iostreams-dev:i386 (1.74.0.3) ... Setting up python3-markupsafe (2.1.2-1+b1) ... Setting up python3-tz (2022.7.1-4) ... Setting up librsvg2-2:i386 (2.54.7+dfsg-1~deb12u1) ... Setting up python3-six (1.16.0-4) ... Setting up python3-pil:i386 (9.4.0-1.1+b1) ... Setting up python3-roman (3.3-3) ... Setting up python3-jinja2 (3.1.2-1) ... Setting up doxygen (1.9.4-4) ... Setting up python3-packaging (23.0-1) ... Setting up python3-certifi (2022.9.24-1) ... Setting up python3-snowballstemmer (2.2.0-2) ... Setting up libpython3.11-dev:i386 (3.11.2-6) ... Setting up python3-greenlet (2.0.2-1) ... Setting up python3-idna (3.3-1) ... Setting up python3-urllib3 (1.26.12-1) ... Setting up imagemagick-6.q16 (8:6.9.11.60+dfsg-1.6) ... update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare (compare) in auto mode update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare-im6 (compare-im6) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate (animate) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate-im6 (animate-im6) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert (convert) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert-im6 (convert-im6) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite (composite) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite-im6 (composite-im6) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure (conjure) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure-im6 (conjure-im6) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import (import) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import-im6 (import-im6) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify (identify) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify-im6 (identify-im6) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream (stream) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream-im6 (stream-im6) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display (display) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display-im6 (display-im6) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage (montage) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage-im6 (montage-im6) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode Setting up texlive-binaries (2022.20220321.62855-5.1+deb12u1) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up python3-dateutil (2.8.2-2) ... 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Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package 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 dpkg-buildpackage: info: source changed by Michael Banck dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean pg_buildext checkcontrol dh clean --with python3 --buildsystem=cmake --parallel debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/rdkit-202209.3' find /build/reproducible-path/rdkit-202209.3 -name "*.pyc" | xargs rm -f rm -f -r Projects/DbCLI/testData/bzr/ rdkit/Chem/inchi.py rm -f -r Docs/Book/_build Code/docs rdkit/docs Code/doxygen_sqlite3.db rm -f \ Code/ForceField/MMFF/test_data/MMFF94_dative_min.sdf \ Code/ForceField/MMFF/test_data/MMFF94_dative_min_from_SMILES.sdf \ Code/ForceField/MMFF/test_data/MMFF94_hypervalent_min.sdf \ Code/ForceField/MMFF/test_data/MMFF94_hypervalent_min_from_SMILES.sdf \ Code/ForceField/MMFF/test_data/MMFF94_reference.log \ Code/ForceField/MMFF/test_data/MMFF94s_reference.log \ Code/ForceField/MMFF/test_data/testMMFFForceField.log \ Code/GraphMol/Depictor/test_data/cis_trans_cpp.out.sdf \ Code/GraphMol/Depictor/test_data/collisions.out.sdf \ Code/GraphMol/Depictor/test_data/first_200.out.sdf \ Code/GraphMol/Depictor/test_data/test1.out.sdf \ Code/GraphMol/FileParsers/test_data/blah.sdf \ Code/GraphMol/FileParsers/test_data/cdk2_stereo.sdf \ Code/GraphMol/FileParsers/test_data/outNCI_few.sdf \ Code/GraphMol/FileParsers/test_data/outNCI_few.tdt \ Code/GraphMol/FileParsers/test_data/outNCI_first_200.props.sdf \ Code/GraphMol/FileParsers/test_data/outSmiles.csv \ Code/GraphMol/ForceFieldHelpers/UFF/test_data/Issue62.sdf \ Code/GraphMol/MolAlign/test_data/ref_e2_pyCrippenO3A.sdf \ Code/GraphMol/SLNParse/lex.yysln.cpp \ Code/GraphMol/SLNParse/sln.tab.cpp \ Code/GraphMol/SLNParse/sln.tab.hpp \ Code/GraphMol/SmilesParse/lex.yysmarts.cpp \ Code/GraphMol/SmilesParse/lex.yysmiles.cpp \ Code/GraphMol/SmilesParse/smarts.tab.cpp \ Code/GraphMol/SmilesParse/smarts.tab.hpp \ Code/GraphMol/SmilesParse/smiles.tab.cpp \ Code/GraphMol/SmilesParse/smiles.tab.hpp \ Code/GraphMol/Wrap/test_data/outNCI_few.sdf \ Code/GraphMol/Wrap/test_data/outSmiles.txt \ Code/RDGeneral/versions.cpp \ Docs/Book/Cartridge.rst \ Docs/Book/Cookbook.rst \ Docs/Book/Install.rst \ Docs/Book/Overview.rst \ rdkit/ML/Data/test_data/testgeneral.dat.pkl \ rdkit/ML/Data/test_data/testquant.qdat.pkl rm -f Code/RDGeneral/versions.h rdkit/sping/tests/testallps.ps dh_auto_clean pg_buildext clean /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit build-%v rm -rf build-*/ make[1]: Leaving directory '/build/reproducible-path/rdkit-202209.3' dh_autoreconf_clean -O--buildsystem=cmake -O--parallel dh_clean -O--buildsystem=cmake -O--parallel debian/rules binary dh binary --with python3 --buildsystem=cmake --parallel dh_update_autotools_config -O--buildsystem=cmake -O--parallel dh_autoreconf -O--buildsystem=cmake -O--parallel debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/rdkit-202209.3' dh_auto_configure -- -DCMAKE_BUILD_TYPE=None -DCMAKE_SKIP_RPATH=ON -DRDK_INSTALL_INTREE=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_BUILD_THREADSAFE_SSS=ON 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-DBoost_NO_BOOST_CMAKE=TRUE -DCMAKE_INSTALL_PREFIX=/usr -DCATCH_DIR=/usr/include/catch2 -DPYTHON_EXECUTABLE=/usr/bin/python3.11 ../ .. -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Catch2: /usr/include/catch2 CATCH: /usr/include/catch2 -- Found PythonInterp: /usr/bin/python3.11 (found version "3.11.2") -- Found PythonLibs: /usr/lib/i386-linux-gnu/libpython3.11.so (found version "3.11.2") :1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives :1: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead CMake Warning at /usr/share/cmake-3.25/Modules/FindBoost.cmake:2217 (message): No header defined for python-py311; skipping header check (note: header-only libraries have no designated component) Call Stack (most recent call first): CMakeLists.txt:304 (find_package) :1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives :1: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead Python Install directory /usr/lib/python3/dist-packages :1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives :1: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead PYTHON Py_ENABLE_SHARED: 1 PYTHON USING LINK LINE: -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 nbval not found, disabling the jupyter tests -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.58.0") found components: system serialization iostreams regex == Using strict rotor definition -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.58.0") found components: system iostreams regex -- maeparser include dir set as '/usr/include' -- maeparser libraries set as '/usr/lib/i386-linux-gnu/libmaeparser.so' -- Found maeparser: /usr/include -- coordgen include dir set as /usr/include -- coordgen libraries set as '/usr/lib/i386-linux-gnu/libcoordgen.so' -- Found coordgen: /usr/include -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.58.0") found components: iostreams regex -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.58.0") found components: system iostreams regex -- Found ZLIB: /usr/lib/i386-linux-gnu/libz.so (found version "1.2.13") == Updating Filters.cpp from pains file == Done updating pains files -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Found Cairo: /usr/include/cairo -- Found Freetype: /usr/lib/i386-linux-gnu/libfreetype.so (found version "2.12.1") -- Could NOT find Boost (missing: program_options) (found suitable version "1.74.0", minimum required is "1.58.0") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY 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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 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++ 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-I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 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-O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 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 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -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 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-I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/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++ 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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' [ 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 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-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 [ 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 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 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/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 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/RDBoost/Wrap.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( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 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' [ 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 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 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' [ 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/Numerics /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Numerics 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/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 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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' cd /build/reproducible-path/rdkit-202209.3/obj-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 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-I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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, 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/RDBoost/Wrap/RDBase.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( | ^~~~~~~~~~~~~~~~~~~~ [ 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" 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/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' [ 7%] Built target testRDValue make -f 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 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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 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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 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'/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, 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/Cluster/Murtagh/Clustering.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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 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' [ 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, 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/DataStructs.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( | ^~~~~~~~~~~~~~~~~~~~ [ 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, 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( | ^~~~~~~~~~~~~~~~~~~~ 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( | ^~~~~~~~~~~~~~~~~~~~ [ 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 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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 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-I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 11%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.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/InfoBitRanker.cpp.o -MF CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp [ 12%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/DataManip/Metric/rdMetricMatrixCalc.so CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.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' [ 12%] Built target rdMetricMatrixCalc make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-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/Data /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/Data /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-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%] 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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ 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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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/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( | ^~~~~~~~~~~~~~~~~~~~ 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/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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ 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( | ^~~~~~~~~~~~~~~~~~~~ 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/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( | ^~~~~~~~~~~~~~~~~~~~ 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: /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("") | ^~~~~~~~~~~~~~~~~~~~~~~ /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' 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= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/build 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, 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: /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/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 make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-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/testGrid.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/build 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' [ 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 [ 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' [ 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' [ 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 [ 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' [ 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' [ 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 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/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( | ^~~~~~~~~~~~~~~~~~~~ [ 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, 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/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' [ 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/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' [ 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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ [ 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' [ 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/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/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' [ 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' [ 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, 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_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/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 [ 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' [ 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 /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] 1666 | if ((tmpChar < 0 || tmpChar > 127) && version > 9000) { | ~~~~~~~~^~~~~ /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 = unsigned char; 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 = 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] [ 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 /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 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/RingInfo.cpp.o -MF CMakeFiles/GraphMol.dir/RingInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RingInfo.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.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/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%] 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 [ 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 [ 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 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/property_map/vector_property_map.hpp:14, from /usr/include/boost/property_map/property_map.hpp:602, from /usr/include/boost/graph/adjacency_list.hpp:27, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ROMol.h:29, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/GraphMol.h:19, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/AdjustQuery.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( | ^~~~~~~~~~~~~~~~~~~~ [ 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 cd /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1 ../../lib/libRDKitGraphMol.so 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 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make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-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[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/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build make[4]: Leaving directory 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-ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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' [ 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 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-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/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' [ 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 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/build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesParseOps.cpp [ 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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ [ 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' [ 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" 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[ 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 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-I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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++ 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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' [ 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' [ 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/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/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' [ 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' [ 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/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/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' [ 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 [ 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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ [ 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, 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/Queries.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( | ^~~~~~~~~~~~~~~~~~~~ [ 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, 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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 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 [ 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 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/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 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'/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, 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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 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 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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, 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/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 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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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 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/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 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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 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 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'/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 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' [ 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' cd /build/reproducible-path/rdkit-202209.3/obj-i686-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 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-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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ [ 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 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 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/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' [ 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, 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/ShapeHelpers/Wrap/rdShapeHelpers.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( | ^~~~~~~~~~~~~~~~~~~~ [ 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, 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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 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' 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, 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( | ^~~~~~~~~~~~~~~~~~~~ [ 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%] 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 [ 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%] 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 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/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/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/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 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -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 [ 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 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/build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/AngleConstraint.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 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 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/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/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build make[4]: Entering directory 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-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 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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%] 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]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-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 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 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' [ 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= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build 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= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-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= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build 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= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/build 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 [ 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= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build 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= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 33%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o cd 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../../../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 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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 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-DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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 test-valgrind make -f 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/test1.cpp.o -MF CMakeFiles/testSubgraphs1.dir/test1.cpp.o.d -o CMakeFiles/testSubgraphs1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs/test1.cpp [ 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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 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 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-I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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-I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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-I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 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 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'/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-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' [ 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 [ 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 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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 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-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 [ 36%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o cd 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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 [ 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 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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' [ 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/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/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' [ 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 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-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' [ 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/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' [ 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 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-I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ [ 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 [ 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' [ 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/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/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' [ 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, 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/Wrap/rdchem.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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 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' [ 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' [ 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 [ 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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ 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/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( | ^~~~~~~~~~~~~~~~~~~~ [ 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, 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/Table.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( | ^~~~~~~~~~~~~~~~~~~~ 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 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 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/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' [ 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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ [ 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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ [ 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= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build 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 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/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( | ^~~~~~~~~~~~~~~~~~~~ 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/Mol.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( | ^~~~~~~~~~~~~~~~~~~~ [ 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' [ 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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ [ 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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ [ 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, 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/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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ /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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ 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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 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' [ 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/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' [ 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' 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' [ 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/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' [ 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, 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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 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' [ 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/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 make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ 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/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( | ^~~~~~~~~~~~~~~~~~~~ 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/DistGeom/Wrap/DistGeom.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 -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, 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/FilterCatalog/Wrap/rdfiltercatalog.h:36, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.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( | ^~~~~~~~~~~~~~~~~~~~ [ 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("") | ^~~~~~~~~~~~~~~~~~~~~~~ /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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ /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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ /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/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( | ^~~~~~~~~~~~~~~~~~~~ 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/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( | ^~~~~~~~~~~~~~~~~~~~ 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: /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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ 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 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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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ 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/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( | ^~~~~~~~~~~~~~~~~~~~ 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/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( | ^~~~~~~~~~~~~~~~~~~~ [ 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 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../../../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 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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 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/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 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-ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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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++ 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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 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-I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -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 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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 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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' [ 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 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/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/graphmolTest1.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[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 External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.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 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/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' [ 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 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-DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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' [ 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 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--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' [ 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' [ 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 [ 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' [ 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' [ 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' [ 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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 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' [ 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 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-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 [ 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 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -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 [ 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' [ 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 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/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' [ 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 [ 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 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 [ 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' [ 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' [ 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 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/usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 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' [ 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' [ 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' [ 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 [ 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' [ 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' [ 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 [ 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' [ 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' [ 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 [ 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' [ 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' [ 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 [ 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' [ 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' [ 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 [ 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' [ 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' [ 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 [ 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' [ 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' [ 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 [ 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 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' [ 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 [ 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' [ 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' [ 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 [ 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' [ 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' [ 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' [ 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' [ 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 [ 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' [ 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' [ 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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 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' [ 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 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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' [ 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 [ 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 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/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' [ 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 [ 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' [ 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' [ 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 [ 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 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-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 [ 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' [ 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 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/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 [ 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 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-ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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' [ 66%] Built target testGenericGroups make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-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= 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' [ 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 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' [ 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' [ 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 [ 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' [ 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' [ 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 [ 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' [ 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' [ 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 [ 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 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/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' [ 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' [ 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 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'/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' [ 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 [ 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' [ 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' [ 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' [ 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= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' 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' [ 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' [ 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' [ 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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 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' [ 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' [ 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' [ 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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ [ 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' [ 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' [ 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 [ 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' [ 68%] Built target testFingerprints make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-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]: 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]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 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 [ 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, 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: /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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ [ 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 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/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 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/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 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-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 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/build/reproducible-path/rdkit-202209.3/obj-i686-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' [ 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 [ 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' [ 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 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-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 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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 [ 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' [ 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/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' [ 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' [ 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, 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/rdmolfiles.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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 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 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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 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testAbbreviations [ 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 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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%] 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 /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) { | ~~^~~~~~~~~~ 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( | ^~~~~~~~~~~~~~~~~~~~ [ 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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ 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/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, 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/SmilesMolSupplier.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%] 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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ 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/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( | ^~~~~~~~~~~~~~~~~~~~ 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, 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/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/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 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' [ 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 /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, | ~~^ ~~~~~~~~~~~ | | | | long unsigned int std::vector >::size_type {aka unsigned int} | %u /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'void testFileSDF_RandomSet_SMI(const char*, const char*)': /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:1232:27: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] 1232 | fprintf(fcsv, "%u;%lu;%s;%.3f;%u;%u;%s;", n, mols.size(), | ~~^ ~~~~~~~~~~~ | | | | long unsigned int std::vector >::size_type {aka unsigned int} | %u /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:1244:27: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] 1244 | fprintf(fcsv, "%u;%lu;%s;%.3f;%u;%u;%s\n", n, mols.size(), | ~~^ ~~~~~~~~~~~ | | | | long unsigned int std::vector >::size_type {aka unsigned int} | %u /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'void testFileSDF_RandomSet(const char*, const char*)': /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:1350:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] 1350 | fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), | ~~^ ~~~~~~~~~~~ | | | | long unsigned int std::vector >::size_type {aka unsigned int} | %u /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:1403:27: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] 1403 | fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), | ~~^ ~~~~~~~~~~~ | | | | long unsigned int std::vector >::size_type {aka unsigned int} | %u /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:1492:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] 1492 | fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), | ~~^ ~~~~~~~~~~~ | | | | long unsigned int std::vector >::size_type {aka unsigned int} | %u 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: /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/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 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../../../../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%] 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 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-DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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-DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 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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 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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 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-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 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 && 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/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 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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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 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 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../../../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 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'/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 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 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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 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 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=. 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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 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../../../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' [ 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 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/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' [ 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 [ 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, 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/Descriptors/Wrap/rdMolDescriptors.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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 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' [ 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/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' [ 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, 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/MolAlign/Wrap/rdMolAlign.cpp:14: /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( | ^~~~~~~~~~~~~~~~~~~~ /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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:446:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] 446 | (python::len(refCrippenContribs) == refNAtoms)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp: In function 'boost::python::tuple RDKit::MolAlign::getCrippenO3AForConfs(RDKit::ROMol&, RDKit::ROMol&, int, boost::python::list, boost::python::list, int, bool, unsigned int, unsigned int, boost::python::list, boost::python::list)': /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:507:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] 507 | (python::len(prbCrippenContribs) == prbNAtoms)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 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 && 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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 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-ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 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-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 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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 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/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' [ 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 [ 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' [ 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' [ 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, 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/RGroupDecomposition/Wrap/rdRGroupComposition.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( | ^~~~~~~~~~~~~~~~~~~~ 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/MolHash/Wrap/rdMolHash.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( | ^~~~~~~~~~~~~~~~~~~~ [ 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' [ 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' [ 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[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/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[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-i686-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]: 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[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 -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[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 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' [ 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 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'/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 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-I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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' [ 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' [ 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 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/MolStandardize/MolStandardize.h:20, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/MolStandardize.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( | ^~~~~~~~~~~~~~~~~~~~ [ 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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ [ 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 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, 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/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, 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/MolOps.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%] 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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ [ 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 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[ 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 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-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 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-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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ [ 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' [ 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 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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 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-ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 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 [ 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 [ 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, 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/Deprotect/Wrap/rdDeprotect.h:15, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Wrap/rdDeprotect.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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 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 [ 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' [ 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, 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/Deprotect/Wrap/DeprotectWrap.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 /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/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( | ^~~~~~~~~~~~~~~~~~~~ [ 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 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-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 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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%] 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 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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 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -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 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../../../../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 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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 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'/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' [ 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[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' 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 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 [ 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' [ 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' [ 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 [ 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' [ 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' [ 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 [ 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' [ 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' [ 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' [ 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' [ 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 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= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f 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-I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 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Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build 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 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%] 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/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]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 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 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/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/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/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, 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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 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 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' 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, 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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 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%] 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/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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [ 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, 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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 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 [ 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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ 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/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, 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/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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ /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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [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' [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/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' cd /build/reproducible-path/rdkit-202209.3/obj-i686-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 -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/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' 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/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, 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/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( | ^~~~~~~~~~~~~~~~~~~~ [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, 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( | ^~~~~~~~~~~~~~~~~~~~ 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/SubstructLibrary/Wrap/rdSubstructLibrary.h:36, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [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' [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, | ^~~~~~~~~~~~ /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp:159:24: note: recursive call 159 | return countMatches(query, startIdx, endIdx, recursionPossible, useChirality, useQueryQueryMatches, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 | numThreads); | ~~~~~~~~~~~ /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::TautomerQuery]': /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, | ^~~~~~~~~~~~ /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp:159:24: note: recursive call 159 | return countMatches(query, startIdx, endIdx, recursionPossible, useChirality, useQueryQueryMatches, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 | numThreads); | ~~~~~~~~~~~ /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::ROMol]': /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, | ^~~~~~~~~~~~ /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp:159:24: note: recursive call 159 | return countMatches(query, startIdx, endIdx, recursionPossible, useChirality, useQueryQueryMatches, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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' [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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' [100%] Built target rdSubstructLibrary make[3]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' STATIC_LINK=0 RDKIT_LIBDIR=/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu//lib pg_buildext build /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit build-%v ### PostgreSQL 15 build ### make[2]: Entering directory '/build/reproducible-path/rdkit-202209.3/build-15' gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o rdkit_io.o /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_io.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o mol_op.o /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c: In function 'mol_murckoscaffold': /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c:312:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 312 | CROMol scaffold = MolMurckoScaffold(mol); | ^~~~~~ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c: In function 'mol_nm_hash': /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c:332:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 332 | char *str = computeNMMolHash(mol, opts); | ^~~~ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c:334:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 334 | char *res = pnstrdup(str, strlen(str)); | ^~~~ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c:327:7: warning: unused variable 'len' [-Wunused-variable] 327 | int len; | ^~~ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c: In function 'mol_adjust_query_properties': /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c:347:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 347 | char *data = PG_GETARG_CSTRING(1); | ^~~~ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c:353:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 353 | Mol *res = deconstructROMol(adj); | ^~~ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c: In function 'mol_to_svg': /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c:368:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 368 | char *legend = PG_GETARG_CSTRING(1); | ^~~~ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_smiles': /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c:392:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 392 | char *res = pnstrdup(str, strlen(str)); | ^~~~ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_mol2s_transition': /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c:460:5: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 460 | text *ts = (text *)palloc(ts_size); // new return value | ^~~~ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c:480:5: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 480 | char *smiles = makeMolText(mol, &len, false, false); | ^~~~ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_mols': /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c:518:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 518 | int32 ts_size = VARHDRSZ + strlen(str); | ^~~~~ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_smiles_transition': /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c:424:1: warning: control reaches end of non-void function [-Wreturn-type] 424 | } | ^ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c: In function 'fmcs_mol_transition': /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c:559:1: warning: control reaches end of non-void function [-Wreturn-type] 559 | } | ^ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o bfp_op.o /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/bfp_op.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o sfp_op.o /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/sfp_op.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o rxn_op.o /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rxn_op.c /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rxn_op.c:164:1: warning: multi-line comment [-Wcomment] 164 | // /* keep compiler quiet - no extra ; */ \ | ^ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rxn_op.c: In function 'reaction_to_svg': /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rxn_op.c:179:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 179 | bool highlightByReactants = PG_GETARG_BOOL(1); | ^~~~ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o rdkit_gist.o /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_gist.c /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_gist.c: In function 'soergeldistsign': /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_gist.c:240:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 240 | uint8 *as = (uint8 *)VARDATA(a); | ^~~~~ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_gist.c: In function 'soergeldist': /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_gist.c:262:10: warning: unused variable 'd' [-Wunused-variable] 262 | double d; | ^ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_gist.c: In function 'gmol_consistent': /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_gist.c:526:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 526 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_gist.c:538:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 538 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_gist.c:570:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 570 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_gist.c: In function 'rdkit_consistent': /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_gist.c:658:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 658 | int siglen = SIGLEN(query); | ^~~ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_gist.c:673:5: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 673 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_gist.c: In function 'gsfp_consistent': /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_gist.c:708:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 708 | int sum, overlapSum, overlapN; | ^~~ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_gist.c:714:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 714 | int nKey = (ISALLTRUE(key)) ? | ^~~ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_gist.c: In function 'greaction_consistent': /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_gist.c:787:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 787 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_gist.c:804:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 804 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_gist.c:832:7: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 832 | uint8 *k = (uint8 *)VARDATA(key); | ^~~~~ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_gist.c: At top level: /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_gist.c:646:1: warning: 'rdkit_consistent' defined but not used [-Wunused-function] 646 | rdkit_consistent(GISTENTRY *entry, StrategyNumber strategy, bytea *key, bytea *query) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_gist.c:261:1: warning: 'soergeldist' defined but not used [-Wunused-function] 261 | soergeldist(bytea *a, bytea *b) { | ^~~~~~~~~~~ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o bfp_gist.o /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/bfp_gist.c /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/bfp_gist.c: In function 'merge_key': /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/bfp_gist.c:698:3: warning: ISO C90 forbids mixed declarations and code [-Wdeclaration-after-statement] 698 | int siglen = GBFP_INNER_SIGLEN(result); | ^~~ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o bfp_gin.o /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/bfp_gin.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o low_gist.o /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/low_gist.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o guc.o /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/guc.c gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o cache.o /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/cache.c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unused-function -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o adapter.o /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/adapter.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/PgSQL/rdkit/adapter.cpp:49: /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( | ^~~~~~~~~~~~~~~~~~~~ gcc -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -fPIC -c -o bitstring.o /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/bitstring.c /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/bitstring.c: In function 'bitstringUnion': /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/bitstring.c:72:7: warning: unused variable 'i' [-Wunused-variable] 72 | int i; | ^ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/bitstring.c: In function 'bitstringIntersection': /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/bitstring.c:106:7: warning: unused variable 'i' [-Wunused-variable] 106 | int i; | ^ g++ -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Werror=vla -Wendif-labels -Wmissing-format-attribute -Wimplicit-fallthrough=3 -Wcast-function-type -Wformat-security -fno-strict-aliasing -fwrapv -fexcess-precision=standard -Wno-format-truncation -Wno-stringop-truncation -g -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -shared -o rdkit.so rdkit_io.o mol_op.o bfp_op.o sfp_op.o rxn_op.o rdkit_gist.o bfp_gist.o bfp_gin.o low_gist.o guc.o cache.o adapter.o bitstring.o -L/usr/lib/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib/llvm-14/lib -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -L/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu//lib -lRDKitMolDraw2D -lRDKitMolTransforms -lRDKitMolHash -lRDKitFMCS -lRDKitChemReactions -lRDKitChemTransforms -lRDKitFileParsers -lRDKitSmilesParse -lRDKitFingerprints -lRDKitSubgraphs -lRDKitDescriptors -lRDKitPartialCharges -lRDKitSubstructMatch -lRDKitGraphMol -lRDKitEigenSolvers -lRDKitDataStructs -lRDKitDepictor -lRDKitRDGeometryLib -lRDKitRDGeneral -pthread sed -e's/@RDKIT_PG_BFP_GIST_FETCH@/FUNCTION 9 gbfp_fetch (internal),/;' \ -e's/@RDKIT_GIN_BFP_TRICONSISTENT@/FUNCTION 6 gin_bfp_triconsistent(internal, int2, bfp, int4, internal, internal, internal),/' \ -e's/@RDKIT_PARALLEL_SAFE@/PARALLEL SAFE/' \ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit.sql.in > rdkit--4.2.0.sql /usr/bin/clang-14 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o rdkit_io.bc /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_io.c /usr/bin/clang-14 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o mol_op.bc /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c:424:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/mol_op.c:559:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ 2 warnings generated. /usr/bin/clang-14 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o bfp_op.bc /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/bfp_op.c /usr/bin/clang-14 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o sfp_op.bc /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/sfp_op.c /usr/bin/clang-14 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o rxn_op.bc /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rxn_op.c /usr/bin/clang-14 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o rdkit_gist.bc /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit_gist.c /usr/bin/clang-14 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o bfp_gist.bc /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/bfp_gist.c /usr/bin/clang-14 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o bfp_gin.bc /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/bfp_gin.c /usr/bin/clang-14 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o low_gist.bc /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/low_gist.c /usr/bin/clang-14 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o guc.bc /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/guc.c /usr/bin/clang-14 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o cache.bc /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/cache.c /usr/bin/clang-14 -std=c++17 -xc++ -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -emit-llvm -c -o adapter.bc /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/adapter.cpp /usr/lib/llvm-14/bin/opt -module-summary -f adapter.bc -o adapter.bc /usr/bin/clang-14 -Wno-ignored-attributes -fno-strict-aliasing -fwrapv -Wno-unused-command-line-argument -Wno-compound-token-split-by-macro -O2 -I/usr/local/include -I/build/reproducible-path/rdkit-202209.3/Code -DRDKITVER='"007300"' -DRDK_TOOLKIT_VERSION='"2022.09.01"' -I. -I/build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit -I/usr/include/postgresql/15/server -I/usr/include/postgresql/internal -Wdate-time -D_FORTIFY_SOURCE=2 -D_GNU_SOURCE -I/usr/include/libxml2 -flto=thin -emit-llvm -c -o bitstring.bc /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/bitstring.c make[2]: Leaving directory '/build/reproducible-path/rdkit-202209.3/build-15' ### End 15 build ### (cd /build/reproducible-path/rdkit-202209.3/Code; doxygen doxygen/doxygen.config) warning: Tag 'TCL_SUBST' at line 213 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'SYMBOL_CACHE_SIZE' at line 337 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'SHOW_DIRECTORIES' at line 557 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'COLS_IN_ALPHA_INDEX' at line 869 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'HTML_ALIGN_MEMBERS' at line 971 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'USE_INLINE_TREES' at line 1162 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'LATEX_SOURCE_CODE' at line 1327 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'XML_SCHEMA' at line 1425 of file 'doxygen/doxygen.config' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'XML_DTD' at line 1431 of file 'doxygen/doxygen.config' has become obsolete. 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Otherwise you run the risk that the wrong font is being used for dot generated graphs. Doxygen version used: 1.9.4 Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching INPUT for files to process... 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Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Lipinski.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MolData3Ddescriptors.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MolData3Ddescriptors.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MolDescriptors.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MolDescriptors.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MolDescriptors3D.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MolDescriptors3D.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MolSurf.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MolSurf.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MORSE.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MORSE.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MQN.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MQN.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/PBF.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/PBF.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/PMI.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/PMI.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Property.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Property.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RegisterDescriptor.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RegisterDescriptor.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/USRDescriptor.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/USRDescriptor.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/WHIM.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/WHIM.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/details.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/details.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DetermineBonds/DetermineBonds.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DetermineBonds/DetermineBonds.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Embedder.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Embedder.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/CDXMLParser.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/CDXMLParser.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/FileParsers.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/FileParsers.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/FileParserUtils.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/FileParserUtils.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/GeneralFileReader.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/GeneralFileReader.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MolFileStereochem.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MolFileStereochem.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MolSGroupParsing.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MolSGroupParsing.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MolSGroupWriting.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MolSGroupWriting.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MolSupplier.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MolWriters.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MolWriters.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MultithreadedMolSupplier.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MultithreadedMolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/PNGParser.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/PNGParser.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/ProximityBonds.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/ProximityBonds.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SequenceParsers.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SequenceParsers.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SequenceWriters.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SequenceWriters.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalog.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalog.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatchers.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatchers.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Filters.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Filters.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairGenerator.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairGenerator.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairs.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairs.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintGenerator.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintGenerator.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Fingerprints.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Fingerprints.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintUtil.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintUtil.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MACCS.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MACCS.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MHFP.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MHFP.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganFingerprints.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganFingerprints.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganGenerator.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganGenerator.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Composition2N.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Composition2N.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/DebugTrace.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/DebugTrace.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/DuplicatedSeedCache.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/DuplicatedSeedCache.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/FMCS.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/FMCS.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Graph.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Graph.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/MatchTable.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/MatchTable.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/MaximumCommonSubgraph.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/MaximumCommonSubgraph.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/RingMatchTableSet.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/RingMatchTableSet.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Seed.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Seed.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/SeedSet.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/SeedSet.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/SubstructMatchCustom.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/SubstructMatchCustom.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/SubstructureCache.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/SubstructureCache.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Target.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Target.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/TargetMatch.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/TargetMatch.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/FFConvenience.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/FFConvenience.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/UFF/Builder.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/UFF/Builder.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/UFF/UFF.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/UFF/UFF.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatGenerator.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatGenerator.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatParams.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatParams.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragFPGenerator.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragFPGenerator.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/GenericGroups/GenericGroups.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/GenericGroups/GenericGroups.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/GraphMol.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/GraphMol.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/MMPA.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/MMPA.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/AlignMolecules.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/AlignMolecules.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/O3AAlignMolecules.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/O3AAlignMolecules.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolBundle.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolBundle.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/MolCatalog.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/MolCatalog.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/MolCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/MolCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/MolCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/MolCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/AtomSymbol.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/AtomSymbol.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawAnnotation.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawAnnotation.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawMol.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawMol.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawMolMCH.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawMolMCH.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawShape.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawShape.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawText.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawText.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextCair/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:219: warning: unbalanced grouping commands o.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextCairo.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextFT.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextFT.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextFTCairo.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextFTCairo.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextFTJS.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextFTJS.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextFTSVG.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextFTSVG.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextJS.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextJS.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextNotFT.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextNotFT.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextSVG.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextSVG.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Fonts/roboto_regular.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Fonts/roboto_regular.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Fonts/telex_regular.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Fonts/telex_regular.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DCairo.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DCairo.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DJS.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DJS.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DSVG.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DUtils.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DUtils.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2Dwx.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2Dwx.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Qt/DrawTextFTQt.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Qt/DrawTextFTQt.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Qt/DrawTextQt.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Qt/DrawTextQt.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Qt/MolDraw2DQt.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Qt/MolDraw2DQt.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/StringRect.h... Parsing file /build/rep/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolOps.h:427: warning: unbalanced grouping commands /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolOps.h:661: warning: unbalanced grouping commands roducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/StringRect.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/LinkNode.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/LinkNode.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/mf.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/mf.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/MolHash.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/MolHash.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/nmmolhash.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/nmmolhash.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange/details.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange/details.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange/MolInterchange.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange/MolInterchange.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolOps.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolOps.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolPickler.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolPickler.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Charge.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Charge.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Fragment.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Fragment.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Metal.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Metal.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/MolStandardize.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/MolStandardize.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Normalize.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Normalize.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Tautomer.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Tautomer.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Validate.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Validate.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/MolTransforms.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/MolTransforms.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MonomerInfo.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MonomerInfo.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/new_canon.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/new_canon.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/GasteigerCharges.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/GasteigerCharges.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/GasteigerParams.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/GasteigerParams.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PeriodicTable.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PeriodicTable.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/QueryAtom.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/QueryAtom.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/QueryBond.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/QueryBond.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/QueryOps.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/QueryOps.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitQueries.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitQueries.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/ReducedGraphs.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ROMol.h:408: warning: unbalanced grouping commands /ReducedGraphs/ReducedGraphs.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Resonance.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Resonance.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupCore.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupCore.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupData.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupData.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupDecompData.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupDecompData.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupGa.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupGa.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupMatch.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupMatch.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupScore.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupScore.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RingInfo.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RingInfo.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Rings.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Rings.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ROMol.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ROMol.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RWMol.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RWMol.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SanitException.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SanitException.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/detail.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/detail.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/ShapeEncoder.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/ShapeEncoder.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/ShapeUtils.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/ShapeUtils.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/SLNAttribs.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/SLNAttribs.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/SLNParse.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/SLNParse.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/SLNParseOps.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/SLNParseOps.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/primes.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/primes.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmartsWrite.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmartsWrite.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesParse.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesParse.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesParseOps.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesParseOps.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesWrite.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesWrite.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/StereoGroup.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/StereoGroup.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/StructChecker/Pattern.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/StructChecker/Pattern.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/StructChecker/ReCharge.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/StructChecker/ReCharge.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/StructChecker/Stereo.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/StructChecker/Stereo.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/StructChecker/StripSmallFragments.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/StructChecker/StripSmallFragments.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/StructChecker/StructChecker.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/StructChecker/StructChecker.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/StructChecker/StructCheckerOptions.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/StructChecker/StructCheckerOptions.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/StructChecker/Tautomer.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/StructChecker/Tautomer.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/StructChecker/Utilites.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/StructChecker/Utilites.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs/Subgraphs.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs/Subgraphs.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs/SubgraphUtils.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs/SubgraphUtils.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstanceGroup.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstanceGroup.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/SubstructMatch.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/SubstructMatch.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/SubstructUtils.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/SubstructUtils.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/PatternFactory.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/PatternFactory.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/SubstructLibrary.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/SubstructLibrary.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery/TautomerQuery.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery/TautomerQuery.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/Snapshot.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/Snapshot.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/Trajectory.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/Trajectory.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Catalogs/Catalog.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/Catalogs/Catalog.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Catalogs/CatalogEntry.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/Catalogs/CatalogEntry.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Catalogs/CatalogParams.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/Catalogs/CatalogParams.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/DataStructs/base64.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/DataStructs/base64.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/DataStructs/BitOps.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/DataStructs/BitOps.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/DataStructs/BitVect.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/DataStructs/BitVect.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/DataStructs/BitVects.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/DataStructs/BitVects.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/DataStructs/BitVectUtils.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/DataStructs/BitVectUtils.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/DataStructs/DatastructsException.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/DataStructs/DatastructsException.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/DataStructs/DatastructsStreamOps.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/DataStructs/DatastructsStreamOps.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/DataStructs/DiscreteDistMat.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/DataStructs/DiscreteDistMat.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/DataStructs/DiscreteValueVect.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/DataStructs/DiscreteValueVect.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/DataStructs/ExplicitBitVect.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/DataStructs/ExplicitBitVect.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/DataStructs/FPBReader.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/DataStructs/FPBReader.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/DataStructs/MultiFPBReader.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/DataStructs/MultiFPBReader.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/DataStructs/SparseBitVect.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/DataStructs/SparseBitVect.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/DataStructs/SparseIntVect.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/DataStructs/SparseIntVect.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Query/AndQuery.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/Query/AndQuery.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Query/EqualityQuery.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/Query/EqualityQuery.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Query/GreaterEqualQuery.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/Query/GreaterEqualQuery.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Query/GreaterQuery.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/Query/GreaterQuery.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Query/LessEqualQuery.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/Query/LessEqualQuery.h... 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Parsing file /build/reproducible-path/rdkit-202209.3/Code/DataManip/MetricMatrixCalc/MetricFuncs.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/DataManip/MetricMatrixCalc/MetricMatrixCalc.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/DataManip/MetricMatrixCalc/MetricMatrixCalc.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/DistPicker.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/DistPicker.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/HierarchicalClusterPicker.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/HierarchicalClusterPicker.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/LeaderPicker.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/LeaderPicker.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/MaxMinPicker.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/MaxMinPicker.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/BadFileException.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/BadFileException.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/BoostEndInclude.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/BoostEndInclude.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/BoostStartInclude.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/BoostStartInclude.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/ConcurrentQueue.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/ConcurrentQueue.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h... 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Parsing file /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/LocaleSwitcher.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Ranking.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Ranking.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDAny.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDAny.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDConfig.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDConfig.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDExportMacros.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDExportMacros.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDProps.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDProps.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDThreads.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDThreads.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDValue-doublemagic.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDValue-doublemagic.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDValue-taggedunion.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDValue-taggedunion.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDValue.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDValue.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/StreamOps.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/StreamOps.h... 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Parsing file /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/DistanceConstraint.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/Nonbonded.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/Nonbonded.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/OopBend.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/OopBend.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/Params.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/Params.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/PositionConstraint.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/PositionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/StretchBend.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/StretchBend.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/TorsionAngle.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/TorsionAngle.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/TorsionConstraint.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/TorsionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/AngleBend.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/AngleBend.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/AngleConstraint.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/AngleConstraint.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/BondStretch.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/BondStretch.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/Contribs.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/Contribs.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/DistanceConstraint.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/DistanceConstraint.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/Inversion.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/Inversion.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/Nonbonded.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/Nonbonded.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/Params.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/Params.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/PositionConstraint.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/PositionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/TorsionAngle.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/TorsionAngle.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/TorsionConstraint.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/TorsionConstraint.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/AlignPoints.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/AlignPoints.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Numerics/Conrec.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/Numerics/Conrec.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Numerics/EigenSolvers/PowerEigenSolver.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/Numerics/EigenSolvers/PowerEigenSolver.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Numerics/Matrix.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/Numerics/Matrix.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer/BFGSOpt.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer/BFGSOpt.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Numerics/SquareMatrix.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/Numerics/SquareMatrix.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Numerics/SymmMatrix.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/Numerics/SymmMatrix.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Geometry/Grid3D.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/Geometry/Grid3D.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Geometry/GridUtils.h... Parsing f/build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h:62: warning: documented symbol 'for experimental torsion angle RDKit::DGeomHelpers::preferences' was not declared or defined. /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:86: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:141: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:210: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:76: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:131: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:200: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:83: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:138: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:207: warning: Found unknown command '\override' /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' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:79: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:134: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:203: warning: Found unknown command '\override' ile /build/reproducible-path/rdkit-202209.3/Code/Geometry/GridUtils.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Geometry/Transform.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/Geometry/Transform.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Geometry/Transform2D.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/Geometry/Transform2D.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Geometry/Transform3D.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/Geometry/Transform3D.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Geometry/UniformGrid3D.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/Geometry/UniformGrid3D.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Geometry/Utils.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/Geometry/Utils.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/Features/Feature.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/Features/Feature.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/ChemicalFeature.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/ChemicalFeature.h... Preprocessing /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/FreeChemicalFeature.h... Parsing file /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/FreeChemicalFeature.h... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Building concept list... Computing nesting relations for classes... Associating documentation with classes... Associating documentation with concepts... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Sorting lists... Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Setting anonymous enum type... Computing dependencies between directories... Generating citations page... Counting members... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Correcting members for VHDL... Computing tooltip texts... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file Catalog.h... Generating code for file CatalogEntry.h... Generating code for file CatalogParams.h... Generating code for file ChemicalFeature.h... Generating code for file FreeChemicalFeature.h... Generating code for file MetricFuncs.h... Generating code for file MetricMatrixCalc.h... Generating code for file base64.h... Generating code for file BitOps.h... Generating code for file BitVect.h... Generating code for file BitVects.h... Generating code for file BitVectUtils.h... Generating code for file DatastructsException.h... Generating code for file DatastructsStreamOps.h... Generating code for file DiscreteDistMat.h... Generating code for file DiscreteValueVect.h... Generating code for file ExplicitBitVect.h... Generating code for file FPBReader.h... Generating code for file MultiFPBReader.h... Generating code for file SparseBitVect.h... Generating code for file SparseIntVect.h... Generating code for file BoundsMatrix.h... Generating code for file ChiralSet.h... Generating code for file ChiralViolationContrib.h... Generating code for file DistGeomUtils.h... Generating code for file DistViolationContrib.h... Generating code for file FourthDimContrib.h... Generating code for file TriangleSmooth.h... Generating code for file Feature.h... Generating code for file Contrib.h... Generating code for file ForceField.h... Generating code for file AngleBend.h... Generating code for file AngleBend.h... Generating code for file AngleConstraint.h... Generating code for file AngleConstraint.h... Generating code for file BondStretch.h... Generating code for file BondStretch.h... Generating code for file Contribs.h... Generating code for file Contribs.h... Generating code for file DistanceConstraint.h... Generating code for file DistanceConstraint.h... Generating code for file Nonbonded.h... Generating code for file Nonbonded.h... Generating code for file OopBend.h... Generating code for file Params.h... Generating code for file Params.h... Generating code for file PositionConstraint.h... Generating code for file PositionConstraint.h... Generating code for file StretchBend.h... Generating code for file TorsionAngle.h... Generating code for file TorsionAngle.h... Generating code for file TorsionConstraint.h... Generating code for file TorsionConstraint.h... Generating code for file Inversion.h... Generating code for file Grid3D.h... Generating code for file GridUtils.h... Generating code for file point.h... Generating code for file Transform.h... Generating code for file Transform2D.h... Generating code for file Transform3D.h... Generating code for file UniformGrid3D.h... Generating code for file Utils.h... Generating code for file Abbreviations.h... Generating code for file Atom.h... Generating code for file atomic_data.h... Generating code for file AtomIterators.h... Generating code for file Bond.h... Generating code for file BondIterators.h... Generating code for file Canon.h... Generating code for file CartesianProduct.h... Generating code for file Enumerate.h... Generating code for file EnumerateBase.h... Generating code for file EnumerateTypes.h... Generating code for file EnumerationPickler.h... Generating code for file EnumerationStrategyBase.h... Generating code for file EvenSamplePairs.h... Generating code for file RandomSample.h... Generating code for file RandomSampleAllBBs.h... Generating code for file PreprocessRxn.h... Generating code for file Reaction.h... Generating code for file ReactionFingerprints.h... Generating code for file ReactionParser.h... Generating code for file ReactionPickler.h... Generating code for file ReactionRunner.h... Generating code for file ReactionUtils.h... Generating code for file SanitizeRxn.h... Generating code for file ChemTransforms.h... Generating code for file MolFragmenter.h... Generating code for file Chirality.h... Generating code for file CIPLabeler.h... Generating code for file CIPMol.h... Generating code for file Configuration.h... Generating code for file Sp2Bond.h... Generating code for file Tetrahedral.h... Generating code for file Descriptor.h... Generating code for file Digraph.h... Generating code for file Edge.h... Generating code for file Mancude.h... Generating code for file Node.h... Generating code for file Priority.h... Generating code for file Pairlist.h... Generating code for file Rule1a.h... Generating code for file Rule1b.h... Generating code for file Rule2.h... Generating code for file Rule3.h... Generating code for file Rule4a.h... Generating code for file Rule4b.h... Generating code for file Rule4c.h... Generating code for file Rule5.h... Generating code for file Rule5New.h... Generating code for file Rule6.h... Generating code for file Rules.h... Generating code for file SequenceRule.h... Generating code for file Sort.h... Generating code for file TooManyNodesException.h... Generating code for file Conformer.h... Generating code for file DepictUtils.h... Generating code for file EmbeddedFrag.h... Generating code for file RDDepictor.h... Generating code for file Deprotect.h... Generating code for file AtomFeat.h... Generating code for file AUTOCORR2D.h... Generating code for file AUTOCORR3D.h... Generating code for file BCUT.h... Generating code for file ConnectivityDescriptors.h... Generating code for file CoulombMat.h... Generating code for file Crippen.h... Generating code for file Data3Ddescriptors.h... Generating code for file EEM.h... Generating code for file GETAWAY.h... Generating code for file Lipinski.h... Generating code for file MolData3Ddescriptors.h... Generating code for file MolDescriptors.h... Generating code for file MolDescriptors3D.h... Generating code for file MolSurf.h... Generating code for file MORSE.h... Generating code for file MQN.h... Generating code for file PBF.h... Generating code for file PMI.h... Generating code for file Property.h... Generating code for file RDF.h... 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... Generating code for file CDXMLParser.h... Generating code for file FileParsers.h... Generating code for file FileParserUtils.h... Generating code for file GeneralFileReader.h... Generating code for file MolFileStereochem.h... Generating code for file MolSGroupParsing.h... Generating code for file MolSGroupWriting.h... Generating code for file MolSupplier.h... Generating code for file MolWriters.h... Generating code for file MultithreadedMolSupplier.h... Generating code for file MultithreadedSDMolSupplier.h... Generating code for file MultithreadedSmilesMolSupplier.h... Generating code for file PNGParser.h... Generating code for file ProximityBonds.h... Generating code for file SequenceParsers.h... Generating code for file SequenceWriters.h... Generating code for file FilterCatalog.h... Generating code for file FilterCatalogEntry.h... Generating code for file FilterMatcherBase.h... Generating code for file FilterMatchers.h... Generating code for file Filters.h... Generating code for file FunctionalGroupHierarchy.h... Generating code for file AtomPairGenerator.h... Generating code for file AtomPairs.h... Generating code for file FingerprintGenerator.h... Generating code for file Fingerprints.h... Generating code for file FingerprintUtil.h... Generating code for file MACCS.h... Generating code for file MHFP.h... Generating code for file MorganFingerprints.h... Generating code for file MorganGenerator.h... Generating code for file RDKitFPGenerator.h... Generating code for file TopologicalTorsionGenerator.h... Generating code for file Composition2N.h... Generating code for file DebugTrace.h... Generating code for file DuplicatedSeedCache.h... Generating code for file FMCS.h... Generating code for file Graph.h... Generating code for file MatchTable.h... Generating code for file MaximumCommonSubgraph.h... Generating code for file RingMatchTableSet.h... Generating code for file Seed.h... Generating code for file SeedSet.h... Generating code for file SubstructMatchCustom.h... Generating code for file SubstructureCache.h... Generating code for file Target.h... Generating code for file TargetMatch.h... Generating code for file TorsionAngleM6.h... Generating code for file TorsionPreferences.h... Generating code for file FFConvenience.h... Generating code for file AtomTyper.h... Generating code for file AtomTyper.h... Generating code for file Builder.h... Generating code for file Builder.h... Generating code for file MMFF.h... Generating code for file UFF.h... Generating code for file FragCatalogEntry.h... Generating code for file FragCatalogUtils.h... Generating code for file FragCatGenerator.h... Generating code for file FragCatParams.h... Generating code for file FragFPGenerator.h... Generating code for file GenericGroups.h... Generating code for file GraphMol.h... Generating code for file MMPA.h... Generating code for file AlignMolecules.h... Generating code for file O3AAlignMolecules.h... Generating code for file MolBundle.h... Generating code for file MolCatalog.h... Generating code for file MolCatalogEntry.h... Generating code for file MolCatalogParams.h... Generating code for file FeatureParser.h... Generating code for file MolChemicalFeature.h... Generating code for file MolChemicalFeatureDef.h... Generating code for file MolChemicalFeatureFactory.h... Generating code for file AtomSymbol.h... Generating code for file DrawAnnotation.h... Generating code for file DrawMol.h... Generating code for file DrawMolMCH.h... Generating code for file DrawShape.h... Generating code for file DrawText.h... Generating code for file DrawTextCairo.h... Generating code for file DrawTextFT.h... Generating code for file DrawTextFTCairo.h... Generating code for file DrawTextFTJS.h... Generating code for file DrawTextFTSVG.h... Generating code for file DrawTextJS.h... Generating code for file DrawTextNotFT.h... Generating code for file DrawTextSVG.h... Generating code for file roboto_regular.h... Generating code for file telex_regular.h... Generating code for file MolDraw2D.h... Generating code for file MolDraw2DCairo.h... Generating code for file MolDraw2DDetails.h... Generating code for file MolDraw2DHelpers.h... Generating code for file MolDraw2DJS.h... Generating code for file MolDraw2DSVG.h... Generating code for file MolDraw2DUtils.h... Generating code for file MolDraw2Dwx.h... Generating code for file DrawTextFTQt.h... Generating code for file DrawTextQt.h... Generating code for file MolDraw2DQt.h... Generating code for file StringRect.h... Generating code for file LinkNode.h... Generating code for file MolEnumerator.h... Generating code for file mf.h... Generating code for file MolHash.h... Generating code for file nmmolhash.h... Generating code for file MolInterchange.h... Generating code for file MolOps.h... Generating code for file MolPickler.h... Generating code for file AcidBaseCatalogEntry.h... Generating code for file AcidBaseCatalogParams.h... Generating code for file AcidBaseCatalogUtils.h... Generating code for file Charge.h... Generating code for file Fragment.h... Generating code for file FragmentCatalogEntry.h... Generating code for file FragmentCatalogParams.h... Generating code for file FragmentCatalogUtils.h... 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... Generating code for file TransformCatalogEntry.h... Generating code for file TransformCatalogParams.h... Generating code for file TransformCatalogUtils.h... Generating code for file Validate.h... Generating code for file MolTransforms.h... Generating code for file MonomerInfo.h... Generating code for file new_canon.h... Generating code for file GasteigerCharges.h... Generating code for file GasteigerParams.h... Generating code for file PeriodicTable.h... Generating code for file QueryAtom.h... Generating code for file QueryBond.h... Generating code for file QueryOps.h... Generating code for file RDKitBase.h... Generating code for file RDKitQueries.h... Generating code for file ReducedGraphs.h... Generating code for file Resonance.h... Generating code for file RGroupCore.h... Generating code for file RGroupData.h... Generating code for file RGroupDecomp.h... Generating code for file RGroupDecompData.h... Generating code for file RGroupFingerprintScore.h... Generating code for file RGroupGa.h... Generating code for file RGroupMatch.h... Generating code for file RGroupScore.h... Generating code for file RGroupUtils.h... Generating code for file RingInfo.h... Generating code for file Rings.h... Generating code for file ROMol.h... Generating code for file RWMol.h... Generating code for file SanitException.h... Generating code for file detail.h... Generating code for file ScaffoldNetwork.h... Generating code for file ShapeEncoder.h... Generating code for file ShapeUtils.h... Generating code for file SLNAttribs.h... Generating code for file SLNParse.h... Generating code for file SLNParseOps.h... Generating code for file primes.h... Generating code for file SmartsWrite.h... Generating code for file SmilesParse.h... Generating code for file SmilesParseOps.h... Generating code for file SmilesWrite.h... Generating code for file StereoGroup.h... Generating code for file Pattern.h... Generating code for file ReCharge.h... Generating code for file Stereo.h... Generating code for file StripSmallFragments.h... Generating code for file StructChecker.h... Generating code for file StructCheckerOptions.h... Generating code for file Utilites.h... Generating code for file Subgraphs.h... Generating code for file SubgraphUtils.h... Generating code for file SubstanceGroup.h... Generating code for file SubstructMatch.h... Generating code for file SubstructUtils.h... Generating code for file PatternFactory.h... Generating code for file SubstructLibrary.h... Generating code for file SubstructLibrarySerialization.h... Generating code for file TautomerQuery.h... Generating code for file Snapshot.h... Generating code for file Trajectory.h... Generating code for file CorrMatGenerator.h... Generating code for file InfoBitRanker.h... Generating code for file InfoGainFuncs.h... Generating code for file AlignPoints.h... Generating code for file Conrec.h... Generating code for file PowerEigenSolver.h... Generating code for file Matrix.h... Generating code for file BFGSOpt.h... Generating code for file SquareMatrix.h... Generating code for file SymmMatrix.h... Generating code for file Vector.h... Generating code for file AndQuery.h... Generating code for file EqualityQuery.h... Generating code for file GreaterEqualQuery.h... Generating code for file GreaterQuery.h... Generating code for file LessEqualQuery.h... Generating code for file LessQuery.h... Generating code for file NullQueryAlgebra.h... Generating code for file OrQuery.h... Generating code for file Query.h... Generating code for file QueryObjects.h... Generating code for file RangeQuery.h... Generating code for file SetQuery.h... Generating code for file XOrQuery.h... Generating code for file boost_numpy.h... Generating code for file import_array.h... Generating code for file pyint_api.h... Generating code for file PySequenceHolder.h... Generating code for file python.h... Generating code for file python_streambuf.h... Generating code for file BadFileException.h... Generating code for file BoostEndInclude.h... Generating code for file BoostStartInclude.h... Generating code for file ConcurrentQueue.h... Generating code for file Dict.h... Generating code for file Exceptions.h... Generating code for file export.h... Generating code for file FileParseException.h... Generating code for file hanoiSort.h... Generating code for file Invariant.h... Generating code for file LocaleSwitcher.h... Generating code for file Ranking.h... Generating code for file RDAny.h... Generating code for file RDConfig.h... Generating code for file RDExportMacros.h... Generating code for file RDLog.h... Generating code for file RDProps.h... Generating code for file RDThreads.h... Generating code for file RDValue-doublemagic.h... Generating code for file RDValue-taggedunion.h... Generating code for file RDValue.h... Generating code for file StreamOps.h... Generating code for file types.h... Generating code for file utils.h... Generating code for file versions.h... Generating code for file DistPicker.h... Generating code for file HierarchicalClusterPicker.h... Generating code for file LeaderPicker.h... Generating code for file MaxMinPicker.h... Generating file documentation... Generating docs for f/build/reproducible-path/rdkit-202209.3/Code/DataStructs/BitOps.h:188: warning: found at different nesting level (7) than expected (4) /build/reproducible-path/rdkit-202209.3/Code/DataStructs/BitOps.h:189: warning: end of comment block while expecting command ile Catalog.h... Generating docs for file CatalogEntry.h... Generating docs for file CatalogParams.h... Generating docs for file ChemicalFeature.h... Generating docs for file FreeChemicalFeature.h... Generating docs for file MetricFuncs.h... Generating docs for file MetricMatrixCalc.h... Generating docs for file base64.h... Generating docs for file BitOps.h... Generating docs for file BitVect.h... Generating docs for file BitVects.h... Generating docs for file BitVectUtils.h... Generating docs for file DatastructsException.h... Generating docs for file DatastructsStreamOps.h... Generating docs for file DiscreteDistMat.h... Generating docs for file DiscreteValueVect.h... Generating docs for file ExplicitBitVect.h... Generating docs for file FPBReader.h... Generating docs for file MultiFPBReader.h... Generating docs for file SparseBitVect.h... Generating docs for file SparseIntVect.h... Generating docs for file BoundsMatrix.h... Generating docs for file ChiralSet.h... Generating docs for file ChiralViolationContrib.h... Generating docs for file DistGeomUtils.h... Generating docs for file DistViolationContrib.h... Generating docs for file FourthDimContrib.h... Generating docs for file TriangleSmooth.h... Generating docs for file Feature.h... Generating docs for file Contrib.h... Generating docs for file ForceField.h... Generating docs for file AngleBend.h... Generating docs for file AngleBend.h... Generating docs for file AngleConstraint.h... Generating docs for file AngleConstraint.h... Generating docs for file BondStretch.h... Generating docs for file BondStretch.h... Generating docs for file Contribs.h... Generating docs for file Contribs.h... 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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... Generating docs for file ReducedGraphs.h... Generating docs for file Resonance.h... Generating docs for file RGroupCore.h... Generating docs for file RGroupData.h... Generating docs for file RGroupDecomp.h... Generating docs for file RGroupDecompData.h... Generating docs for file RGroupFingerprintScore.h... Generating docs for file RGroupGa.h... Generating docs for file RGroupMatch.h... Generating docs for file RGroupScore.h... Generating docs for file RGroupUtils.h... Generating docs for file RingInfo.h... Generating docs for file Rings.h... Generating docs for file ROMol.h... 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Generating docs for file RDProps.h./build/reproducible-path/rdkit-202209.3/Code/DistGeom/DistGeomUtils.h:95: warning: The following parameter of DistGeom::constructForceField(const BoundsMatrix &mmat, RDGeom::PointPtrVect &positions, const VECT_CHIRALSET &csets, double weightChiral=1.0, double weightFourthDim=0.1, std::map< std::pair< int, int >, double > *extraWeights=nullptr, double basinSizeTol=5.0, boost::dynamic_bitset<> *fixedPts=nullptr) is not documented: parameter 'fixedPts' /build/reproducible-path/rdkit-202209.3/Code/ForceField/ForceField.h:159: warning: argument 'snapshotFreq' of command @param is not found in the argument list of ForceFields::ForceField::minimize(unsigned int maxIts=200, double forceTol=1e-4, double energyTol=1e-6) /build/reproducible-path/rdkit-202209.3/Code/ForceField/ForceField.h:159: warning: argument 'snapshotVect' of command @param is not found in the argument list of ForceFields::ForceField::minimize(unsigned int maxIts=200, double forceTol=1e-4, double energyTol=1e-6) /build/reproducible-path/rdkit-202209.3/Code/ForceField/ForceField.h:144: warning: The following parameters of ForceFields::ForceField::minimize(unsigned int snapshotFreq, RDKit::SnapshotVect *snapshotVect, unsigned int maxIts=200, double forceTol=1e-4, double energyTol=1e-6) are not documented: parameter 'snapshotFreq' parameter 'snapshotVect' /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/AngleBend.h:31: warning: argument 'angleType' of command @param is not found in the argument list of ForceFields::MMFF::AngleBendContrib::AngleBendContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, const MMFFAngle *mmffAngleParams, const MMFFProp *mmffPropParamsCentralAtom) /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/AngleBend.h:31: warning: The following parameters of ForceFields::MMFF::AngleBendContrib::AngleBendContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, const MMFFAngle *mmffAngleParams, const MMFFProp *mmffPropParamsCentralAtom) are not documented: parameter 'mmffAngleParams' parameter 'mmffPropParamsCentralAtom' /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/AngleConstraint.h:28: warning: argument 'minAngle' of command @param is not found in the argument list of ForceFields::MMFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/AngleConstraint.h:28: warning: argument 'maxAngle' of command @param is not found in the argument list of ForceFields::MMFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/AngleConstraint.h:28: warning: The following parameters of ForceFields::MMFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) are not documented: parameter 'minAngleDeg' parameter 'maxAngleDeg' /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/BondStretch.h:28: warning: argument 'bondType' of command @param is not found in the argument list of ForceFields::MMFF::BondStretchContrib::BondStretchContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams) /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/BondStretch.h:28: warning: argument 'end1Params' of command @param is not found in the argument list of ForceFields::MMFF::BondStretchContrib::BondStretchContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams) /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/BondStretch.h:28: warning: argument 'end2Params' of command @param is not found in the argument list of ForceFields::MMFF::BondStretchContrib::BondStretchContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams) /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/BondStretch.h:28: warning: The following parameter of ForceFields::MMFF::BondStretchContrib::BondStretchContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const MMFFBond *mmffBondParams) is not documented: parameter 'mmffBondParams' /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/Nonbonded.h:54: warning: The following parameters of ForceFields::MMFF::EleContrib::EleContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, double chargeTerm, std::uint8_t dielModel, bool is1_4) are not documented: parameter 'chargeTerm' parameter 'dielModel' parameter 'is1_4' .. Generating docs for file RDThreads.h... Generating docs for file RDValue-doublemagic.h... Generating docs for file RDValue-taggedunion.h... Generating docs for file RDValue.h... Generating docs for file StreamOps.h... Generating docs for file types.h... Generating docs for file utils.h... Generating docs for file versions.h... Generating docs for file DistPicker.h... Generating docs for file HierarchicalClusterPicker.h... Generating docs for file LeaderPicker.h... Generating docs for file MaxMinPicker.h... Generating page documentation... Generating docs for page deprecated... Generating group documentation... Generating class documentation... Generating docs for compound BitVect... Generating docs for compound Data3Ddescriptors... Generating docs for compound DatastructsException... Generating docs for compound ExplicitBitVect... Generating docs for compound IndexErrorException... Generating docs for compound KeyErrorException... Generating docs for compound MolData3Ddescriptors... 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Generating docs for compound ForceFields::MMFF::AngleConstraintContrib... Generating docs for compound ForceFields::MMFF::BondStretchContrib... Generating docs for compound ForceFields::MMFF::DistanceConstraintContrib... Generating docs for compound ForceFields::MMFF::EleContrib... Generating docs for compound ForceFields::MMFF::MMFFAngle... Generating docs for compound ForceFields::MMFF::MMFFAngleCollection... Generating docs for compound ForceFields::MMFF::MMFFAromCollection... Generating docs for compound ForceFields::MMFF::MMFFBndkCollection... Generating docs for compound ForceFields::MMFF::MMFFBond... Generating docs for compound ForceFields::MMFF::MMFFBondCollection... Generating docs for compound ForceFields::MMFF::MMFFChg... Generating docs for compound ForceFields::MMFF::MMFFChgCollection... Generating docs for compound ForceFields::MMFF::MMFFCovRadPauEle... Generating docs for compound ForceFields::MMFF::MMFFCovRadPauEleCollection... Generating docs for compound ForceFields::MMFF::MMFFDef... Generating docs for compound ForceFields::MMFF::MMFFDefCollection... Generating docs for compound ForceFields::MMFF::MMFFDfsbCollection... Ge/build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/PositionConstraint.h:29: warning: argument 'minDispl' of command @param is not found in the argument list of ForceFields::MMFF::PositionConstraintContrib::PositionConstraintContrib(ForceField *owner, unsigned int idx, double maxDispl, double forceConst) /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/StretchBend.h:32: warning: argument 'angleType' of command @param is not found in the argument list of ForceFields::MMFF::StretchBendContrib::StretchBendContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const MMFFStbn *mmffStbnParams, const MMFFAngle *mmffAngleParams, const MMFFBond *mmffBondParams1, const MMFFBond *mmffBondParams2) /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/StretchBend.h:32: warning: The following parameters of ForceFields::MMFF::StretchBendContrib::StretchBendContrib(ForceField *owner, const unsigned int idx1, const unsigned int idx2, const unsigned int idx3, const MMFFStbn *mmffStbnParams, const MMFFAngle *mmffAngleParams, const MMFFBond *mmffBondParams1, const MMFFBond *mmffBondParams2) are not documented: parameter 'mmffStbnParams' parameter 'mmffAngleParams' parameter 'mmffBondParams1' parameter 'mmffBondParams2' /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/TorsionAngle.h:33: warning: argument 'torsionType' of command @param is not found in the argument list of ForceFields::MMFF::TorsionAngleContrib::TorsionAngleContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, const MMFFTor *mmffTorParams) /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/TorsionAngle.h:33: warning: The following parameter of ForceFields::MMFF::TorsionAngleContrib::TorsionAngleContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, const MMFFTor *mmffTorParams) is not documented: parameter 'mmffTorParams' /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/Nonbonded.h:30: warning: The following parameter of ForceFields::MMFF::VdWContrib::VdWContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, const MMFFVdWRijstarEps *mmffVdWConstants) is not documented: parameter 'mmffVdWConstants' /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/AngleConstraint.h:28: warning: argument 'minAngle' of command @param is not found in the argument list of ForceFields::UFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/AngleConstraint.h:28: warning: argument 'maxAngle' of command @param is not found in the argument list of ForceFields::UFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/AngleConstraint.h:28: warning: The following parameters of ForceFields::UFF::AngleConstraintContrib::AngleConstraintContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, double minAngleDeg, double maxAngleDeg, double forceConst) are not documented: parameter 'minAngleDeg' parameter 'maxAngleDeg' /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/Inversion.h:29: warning: The following parameter of ForceFields::UFF::InversionContrib::InversionContrib(ForceField *owner, unsigned int idx1, unsigned int idx2, unsigned int idx3, unsigned int idx4, int at2AtomicNum, bool isCBoundToO, double oobForceScalingFactor=1.0) is not documented: parameter 'oobForceScalingFactor' /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/PositionConstraint.h:29: warning: argument 'minDispl' of command @param is not found in the argument list of ForceFields::UFF::PositionConstraintContrib::PositionConstraintContrib(ForceField *owner, unsigned int idx, double maxDispl, double forceConst) /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/RDDepictor.h:214: warning: argument 'refPattern' of command @param is not found in the argument list of RDDepict::generateDepictionMatching3DStructure(RDKit::ROMol &mol, const RDKit::ROMol &reference, int confId=-1, RDKit::ROMol *referencePattern=nullptr, bool acceptFailure=false, bool forceRDKit=false) /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/RDDepictor.h:214: warning: The following parameter of RDDepict::generateDepictionMatching3DStructure(RDKit::ROMol &mol, const RDKit::ROMol &reference, int confId=-1, RDKit::ROMol *referencePattern=nullptr, bool acceptFailure=false, bool forceRDKit=false) is not documented: parameter 'referencePattern' nerating docs for compound ForceFields::MMFF::MMFFHerschbachLaurie... Generating docs for compound ForceFields::MMFF::MMFFHerschbachLaurieCollection... Generating docs for compound ForceFields::MMFF::MMFFOop... Generating docs for compound ForceFields::MMFF::MMFFOopCollection... Generating docs for compound ForceFields::MMFF::MMFFPBCI... Generating docs for compound ForceFields::MMFF::MMFFPBCICollection... Generating docs for compound ForceFields::MMFF::MMFFProp... Generating docs for compound ForceFields::MMFF::MMFFPropCollection... Generating docs for compound ForceFields::MMFF::MMFFStbn... Generating docs for compound ForceFields::MMFF::MMFFStbnCollection... Generating docs for compound ForceFields::MMFF::MMFFTor... Generating docs for compound ForceFields::MMFF::MMFFTorCollection... Generating docs for compound ForceFields::MMFF::MMFFVdW... Generating docs for compound ForceFields::MMFF::MMFFVdWCollection... Generating docs for compound ForceFields::MMFF::MMFFVdWRijstarEps... Generating docs for compound ForceFields::MMFF::OopBendContrib... Generating docs for compound ForceFields::MMFF::PositionConstraintContrib... Generating docs for compound ForceFields::MMFF::StretchBendContrib... Generating docs for compound ForceFields::MMFF::TorsionAngleContrib... Generating docs for compound ForceFields::MMFF::TorsionConstraintContrib... Generating docs for compound ForceFields::MMFF::VdWContrib... Generating docs for namespace ForceFields::MMFF::Utils Generating docs for namespace ForceFields::UFF Generating docs for compound ForceFields::UFF::AngleBendContrib... Generating docs for compound ForceFields::UFF::AngleConstraintContrib... Generating docs for compound ForceFields::UFF::AtomicParams... Generating docs for compound ForceFields::UFF::BondStretchContrib... Generating docs for compound ForceFields::UFF::DistanceConstraintContrib... Generating docs for compound ForceFields::UFF::InversionContrib... Generating docs for compound ForceFields::UFF::ParamCollection... Generating docs for compound ForceFields::UFF::PositionConstraintContrib... Generating docs for compound ForceFields::UFF::TorsionAngleContrib... Generating docs for compound ForceFields::UFF::TorsionConstraintContrib... Generating docs for compound ForceFields::UFF::UFFAngle... Generating docs for compound ForceFields::UFF::UFFBond... Generating docs for compound ForceFields::UFF::UFFInv... Generating docs for compound ForceFields::UFF::UFFTor... Generating docs for compound ForceFields::UFF::UFFVdW... Generating docs for compound ForceFields::UFF::vdWContrib... Generating docs for namespace ForceFields::UFF::Params Generating docs for namespace ForceFields::UFF::Utils Generating docs for namespace Invar Generating docs for compound Invar::Invariant... Generating docs for namespace MolTransforms Generating docs for namespace Queries Generating docs for compound Queries::AndQuery... Generating docs for compound Queries::EqualityQuery... Generating docs for compound Queries::GreaterEqualQuery... Generating docs for compound Queries::GreaterQuery... Generating docs for compound Queries::Int2Type... Generating docs for compound Queries::LessEqualQuery... Generating docs for compound Queries::LessQuery... Generating docs for compound Queries::OrQuery... Generating docs for compound Queries::Query... Generating docs for compound Queries::RangeQuery... Generating docs for compound Queries::SetQuery... Generating docs for compound Queries::XOrQuery... Generating docs for namespace Rankers Generating docs for namespace RDCatalog Generating docs for compound RDCatalog::Catalog... Generating docs for compound RDCatalog::CatalogEntry... Generating docs for compound RDCatalog::CatalogParams... Generating docs for compound RDCatalog::HierarchCatalog... Generating docs for nested compound RDCatalog::HierarchCatalog::vertex_entry_t... Generating docs for namespace RDDataManip Generating docs for compound RDDataManip::MetricMatrixCalc... Generating docs for namespace RDDepict Generating docs for compound RDDepict::DepictException... Generating docs for compound RDDepict::Embe/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' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstanceGroup.h:278: warning: The following parameter of RDKit::addSubstanceGroup(ROMol &mol, SubstanceGroup sgroup) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/CDXMLParser.h:43: warning: argument 'fileName' of command @param is not found in the argument list of RDKit::CDXMLFileToMols(const std::string &filename, bool sanitize=true, bool removeHs=true) /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/CDXMLParser.h:43: warning: The following parameter of RDKit::CDXMLFileToMols(const std::string &filename, bool sanitize=true, bool removeHs=true) is not documented: parameter 'filename' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SequenceParsers.h:105: warning: argument 'seq' of command @param is not found in the argument list of RDKit::HELMToMol(const char *helm, bool sanitize=true) /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SequenceParsers.h:105: warning: The following parameter of RDKit::HELMToMol(const char *helm, bool sanitize=true) is not documented: parameter 'helm' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Fingerprints.h:69: warning: The following parameter of RDKit::LayeredFingerprintMol(const ROMol &mol, unsigned int layerFlags=0xFFFFFFFF, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, std::vector< unsigned int > *atomCounts=nullptr, ExplicitBitVect *setOnlyBits=nullptr, bool branchedPaths=true, const std::vector< std::uint32_t > *fromAtoms=nullptr) is not documented: parameter 'fromAtoms' /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' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/FileParsers.h:51: warning: argument 'line' from the argument list of RDKit::MolDataStreamToMol has multiple @param documentation sections /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesWrite.h:161: warning: argument 'doRandom' of command @param is not found in the argument list of RDKit::MolFragmentToSmiles(const ROMol &mol, const std::vector< int > &atomsToUse, const std::vector< int > *bondsToUse=nullptr, const std::vector< std::string > *atomSymbols=nullptr, const std::vector< std::string > *bondSymbols=nullptr, bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false) /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesWrite.h:210: warning: The following parameter of RDKit::MolToCXSmiles(const ROMol &mol, bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false, bool doRandom=false) is not documented: parameter 'doRandom' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/FileParsers.h:341: warning: argument 'fName' of command @param is not found in the argument list of RDKit::MolToPDBFile(const ROMol &mol, const std::string &fname, int confId=-1, unsigned int flavor=0) /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/FileParsers.h:341: warning: The following parameter of RDKit::MolToPDBFile(const ROMol &mol, const std::string &fname, int confId=-1, unsigned int flavor=0) is not documented: parameter 'fname' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesWrite.h:101: warning: The following parameter of RDKit::MolToSmiles(const ROMol &mol, bool doIsomericSmiles=true, bool doKekule=false, int rootedAtAtom=-1, bool canonical=true, bool allBondsExplicit=false, bool allHsExplicit=false, bool doRandom=false) is not documented: parameter 'doRandom' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Fingerprints.h:120: warning: The following parameter of RDKit::PatternFingerprintMol(const ROMol &mol, unsigned int fpSize=2048, std::vector< unsigned int > *atomCounts=nullptr, ExplicitBitVect *setOnlyBits=nullptr, bool tautomericFingerprint=false) is not documented: parameter 'tautomericFingerprint' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Fingerprints.h:27: warning: argument 'useBondOrders' of command @param is not found in the argument list of RDKit::RDKFingerprintMol(const ROMol &mol, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, unsigned int nBitsPerHash=2, bool useHs=true, double tgtDensity=0.0, unsigned int minSize=128, bool branchedPaths=true, bool useBondOrder=true, std::vector< std::uint32_t > *atomInvariants=nullptr, const std::vector< std::uint32_t > *fromAtoms=nullptr, std::vector< std::vector< std::uint32_t > > *atomBits=nullptr, std::map< std::uint32_t, std::vector< std::vector< int > > > *bitInfo=nullptr) /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Fingerprints.h:27: warning: The following parameters of RDKit::RDKFingerprintMol(const ROMol &mol, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, unsigned int nBitsPerHash=2, bool useHs=true, double tgtDensity=0.0, unsigned int minSize=128, bool branchedPaths=true, bool useBondOrder=true, std::vector< std::uint32_t > *atomInvariants=nullptr, const std::vector< std::uint32_t > *fromAtoms=nullptr, std::vector< std::vector< std::uint32_t > > *atomBits=nullptr, std::map< std::uint32_t, std::vector< std::vector< int > > > *bitInfo=nullptr) are not documented: parameter 'useBondOrder' parameter 'bitInfo' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionRunner.h:93: warning: The following parameter of RDKit::reduceProductToSideChains(const ROMOL_SPTR &product, bool addDummyAtoms=true) is not documented: parameter 'product' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms/ChemTransforms.h:114: warning: argument 'useChirality' of command @param is not found in the argument list of RDKit::replaceCore(const ROMol &mol, const ROMol &core, const MatchVectType &matchVect, bool replaceDummies=true, bool labelByIndex=false, bool requireDummyMatch=false) /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionRunner.h:66: warning: argument 'reactantTemplateIdx' of command @param is not found in the argument list of RDKit::run_Reactant(const ChemicalReaction &rxn, const ROMOL_SPTR &reactant, unsigned int reactantIdx) /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionRunner.h:66: warning: The following parameters of RDKit::run_Reactant(const ChemicalReaction &rxn, const ROMOL_SPTR &reactant, unsigned int reactantIdx) are not documented: parameter 'rxn' parameter 'reactantIdx' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/SubstructMatch.h:65: warning: argument 'matchParams' of command @param is not found in the argument list of RDKit::SubstructMatch(const ROMol &mol, const ROMol &query, const SubstructMatchParameters ¶ms=SubstructMatchParameters()) /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/SubstructMatch.h:65: warning: The following parameter of RDKit::SubstructMatch(const ROMol &mol, const ROMol &query, const SubstructMatchParameters ¶ms=SubstructMatchParameters()) is not documented: parameter 'params' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/SubstructMatch.h:78: warning: argument 'matchParams' of command @param is not found in the argument list of RDKit::SubstructMatch(ResonanceMolSupplier &resMolSuppl, const ROMol &query, const SubstructMatchParameters ¶ms=SubstructMatchParameters()) /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/SubstructMatch.h:78: warning: The following parameter of RDKit::SubstructMatch(ResonanceMolSupplier &resMolSuppl, const ROMol &query, const SubstructMatchParameters ¶ms=SubstructMatchParameters()) is not documented: parameter 'params' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/SubstructMatch.h:133: warning: The following parameter of RDKit::SubstructMatch(T1 &mol, const T2 &query, std::vector< MatchVectType > &matchVect, bool uniquify=true, bool recursionPossible=true, bool useChirality=false, bool useQueryQueryMatches=false, unsigned int maxMatches=1000, int numThreads=1) is not documented: parameter 'numThreads' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintGenerator.h:129: warning: The following parameters of RDKit::AtomEnvironment::getBitId(FingerprintArguments< OutputType > *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, const AdditionalOutput *AdditionalOutput, const bool hashResults=false, const std::uint64_t fpSize=0) const=0 are not documented: parameter 'AdditionalOutput' parameter 'fpSize' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Reaction.h:220: warning: argument 'maxProducts' of command @param is not found in the argument list of RDKit::ChemicalReaction::runReactants(const MOL_SPTR_VECT reactants, unsigned int numProducts=1000) const /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Reaction.h:220: warning: The following parameter of RDKit::ChemicalReaction::runReactants(const MOL_SPTR_VECT reactants, unsigned int numProducts=1000) const is not documented: parameter 'numProducts' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatchers.h:430: warning: argument 'matches' of command @param is not found in the argument list of RDKit::ExclusionList::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 101 in file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:101: warning: The following parameter of RDKit::ExclusionList::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' ddedAtom... Generating docs for compound RDDepict::EmbeddedFrag... Generating docs for compound RDDepict::gtIIPair... Generating docs for namespace RDFeatures Generating docs for compound RDFeatures::ExplicitFeature... Generating docs for compound RDFeatures::ImplicitFeature... Generating docs for namespace RDGeom Generating docs for compound RDGeom::Grid3D... Generating docs for compound RDGeom::GridException... Generating docs for compound RDGeom::Point... Generating docs for compound RDGeom::Point2D... Generating docs for compound RDGeom::Point3D... Generating docs for compound RDGeom::PointND... Generating docs for compound RDGeom::Transform2D... Generating docs for compound RDGeom::Transform3D... Generating docs for compound RDGeom::UniformGrid3D... Generating docs for namespace RDInfoTheory Generating docs for compound RDInfoTheory::BitCorrMatGenerator... Generating docs for compound RDInfoTheory::InfoBitRanker... Generating docs for namespace RDKit Generating docs for compound RDKit::AdditionalOutput... Generating docs for compound RDKit::AromaticAtomIterator_... Generating docs for compound RDKit::Atom... Generating docs for compound RDKit::AtomEnvironment... Generating docs for compound RDKit::AtomEnvironmentGenerator... Generating docs for compound RDKit::atomicData... Generating docs for compound RDKit::AtomInvariantsGenerator... Generating docs for compound RDKit::AtomIterator_... Generating docs for compound RDKit::AtomKekulizeException... Generating docs for compound RDKit::AtomMonomerInfo... Generating docs for compound RDKit::AtomPDBResidueInfo... Generating docs for compound RDKit::AtomRingQuery... Generating docs for compound RDKit::AtomSanitizeException... Generating docs for compound RDKit::AtomValenceException... Generating docs for compound RDKit::BadFileException... Generating docs for compound RDKit::Bond... Generating docs for compound RDKit::BondInvariantsGenerator... Generating docs for compound RDKit::BondIterator_... Generating docs for compound RDKit::CachedMolHolder... Generating docs for compound RDKit::CachedSmilesMolHolder... Generating docs for compound RDKit::CachedTrustedSmilesMolHolder... Generating docs for compound RDKit::CartesianProduct... Generating docs for compound RDKit::CartesianProductStrategy... Generating docs for compound RDKit::charptr_functor... Generating docs for compound RDKit::ChemicalReaction... Generating docs for compound RDKit::ChemicalReactionException... Generating docs for compound RDKit::ChemicalReactionParserException... Generating docs for compound RDKit::Conformer... Generating docs for compound RDKit::ConformerException... Generating docs for compound RDKit::ConstBondIterator_... Generating docs for compound RDKit::CustomPropHandler... Generating docs for compound RDKit::CXXAtomIterator... Generating docs for nested compound RDKit::CXXAtomIterator::CXXAtomIter... Generating docs for compound RDKit::CXXBondIterator... Generating docs for nested compound RDKit::CXXBondIterator::CXXBondIter... Generating docs for compound RDKit::DataStructsExplicitBitVecPropHandler... Generating docs for compound RDKit::Dict... Generating docs for nested compound RDKit::Dict::Pair... Generating docs for compound RDKit::DiscreteDistMat... Generating docs for compound RDKit::DiscreteValueVect... Generating docs for compound RDKit::DrawColour... Generating docs for compound RDKit::EnumerateLibrary... Generating docs for compound RDKit::EnumerateLibraryBase... Generating docs for compound RDKit::EnumerationParams... Generating docs for compound RDKit::EnumerationStrategyBase... Generating docs for compound RDKit::EnumerationStrategyException... Generating docs for compound RDKit::EvenSamplePairsStrategy... Generating docs for compound RDKit::ExclusionList... Generating docs for compound RDKit::FeatureFileParseException... Generating docs for compound RDKit::FileParseException... Generating docs for compound RDKit::FilterCatalog... Generating docs for compound RDKit::FilterCatalogEntry... Generating docs for compound RDKit::FilterCatalogParams... Generating docs for compound RD/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:101: warning: argument 'matches' of command @param is not found in the argument list of RDKit::FilterMatcherBase::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const=0 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:101: warning: The following parameter of RDKit::FilterMatcherBase::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const=0 is not documented: parameter 'matchVect' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:71: warning: argument 'highlight_atoms' from the argument list of RDKit::MolDraw2D::drawMolecule has multiple @param documentation sections /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:71: warning: The following parameter of RDKit::MolDraw2D::drawMolecule(const ROMol &mol, const std::string &legend, const std::vector< int > *highlight_atoms, const std::vector< int > *highlight_bonds, const std::map< int, DrawColour > *highlight_atom_map=nullptr, const std::map< int, DrawColour > *highlight_bond_map=nullptr, const std::map< int, double > *highlight_radii=nullptr, int confId=-1) is not documented: parameter 'highlight_bonds' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:144: warning: argument 'highlight_atom_map' of command @param is not found in the argument list of RDKit::MolDraw2D::drawMolecules(const std::vector< ROMol * > &mols, const std::vector< std::string > *legends=nullptr, const std::vector< std::vector< int > > *highlight_atoms=nullptr, const std::vector< std::vector< int > > *highlight_bonds=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_atom_maps=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_bond_maps=nullptr, const std::vector< std::map< int, double > > *highlight_radii=nullptr, const std::vector< int > *confIds=nullptr) /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:144: warning: argument 'highlight_bond_map' of command @param is not found in the argument list of RDKit::MolDraw2D::drawMolecules(const std::vector< ROMol * > &mols, const std::vector< std::string > *legends=nullptr, const std::vector< std::vector< int > > *highlight_atoms=nullptr, const std::vector< std::vector< int > > *highlight_bonds=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_atom_maps=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_bond_maps=nullptr, const std::vector< std::map< int, double > > *highlight_radii=nullptr, const std::vector< int > *confIds=nullptr) /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:144: warning: argument 'confId' of command @param is not found in the argument list of RDKit::MolDraw2D::drawMolecules(const std::vector< ROMol * > &mols, const std::vector< std::string > *legends=nullptr, const std::vector< std::vector< int > > *highlight_atoms=nullptr, const std::vector< std::vector< int > > *highlight_bonds=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_atom_maps=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_bond_maps=nullptr, const std::vector< std::map< int, double > > *highlight_radii=nullptr, const std::vector< int > *confIds=nullptr) /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:144: warning: argument 'highlight_atoms' from the argument list of RDKit::MolDraw2D::drawMolecules has multiple @param documentation sections /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:144: warning: The following parameters of RDKit::MolDraw2D::drawMolecules(const std::vector< ROMol * > &mols, const std::vector< std::string > *legends=nullptr, const std::vector< std::vector< int > > *highlight_atoms=nullptr, const std::vector< std::vector< int > > *highlight_bonds=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_atom_maps=nullptr, const std::vector< std::map< int, DrawColour > > *highlight_bond_maps=nullptr, const std::vector< std::map< int, double > > *highlight_radii=nullptr, const std::vector< int > *confIds=nullptr) are not documented: parameter 'highlight_bonds' parameter 'highlight_atom_maps' parameter 'highlight_bond_maps' parameter 'confIds' Kit::FilterData_t... Generating docs for compound RDKit::FilterHierarchyMatcher... Generating docs for compound RDKit::FilterMatch... Generating docs for compound RDKit::FilterMatcherBase... Generating docs for compound RDKit::FilterProperty_t... Generating docs for compound RDKit::FingerprintArguments... Generating docs for compound RDKit::FingerprintGenerator... Generating docs for compound RDKit::FingerprintVarianceScoreData... Generating docs for compound RDKit::FixedMolSizeMolBundle... Generating docs for compound RDKit::ForwardSDMolSupplier... Generating docs for compound RDKit::FPBReader... Generating docs for compound RDKit::FPHolderBase... Generating docs for compound RDKit::FragCatalogEntry... Generating docs for compound RDKit::FragCatGenerator... Generating docs for compound RDKit::FragCatParams... Generating docs for compound RDKit::FragFPGenerator... Generating docs for compound RDKit::GaResult... Generating docs for compound RDKit::GasteigerParams... Generating docs for compound RDKit::HasPropQuery... Generating docs for compound RDKit::HasPropWithValueQuery... Generating docs for compound RDKit::HasPropWithValueQuery< TargetPtr, ExplicitBitVect >... Generating docs for compound RDKit::HasPropWithValueQuery< TargetPtr, std::string >... Generating docs for compound RDKit::HeteroatomIterator_... Generating docs for compound RDKit::KekulizeException... Generating docs for compound RDKit::KeyFromPropHolder... Generating docs for compound RDKit::KeyHolderBase... Generating docs for compound RDKit::larger_of... Generating docs for compound RDKit::ltDouble... Generating docs for compound RDKit::MatchingAtomIterator_... Generating docs for compound RDKit::MCSAtomCompareParameters... Generating docs for compound RDKit::MCSBondCompareParameters... Generating docs for compound RDKit::MCSParameters... Generating docs for compound RDKit::MCSProgressData... Generating docs for compound RDKit::MCSResult... Generating docs for compound RDKit::MolBundle... Generating docs for compound RDKit::MolCatalogEntry... Generating docs for compound RDKit::MolCatalogParams... Generating docs for compound RDKit::MolChemicalFeature... Generating docs for compound RDKit::MolChemicalFeatureDef... Generating docs for compound RDKit::MolChemicalFeatureFactory... Generating docs for compound RDKit::MolDraw2D... Generating docs for compound RDKit::MolDraw2DCairo... Generating docs for compound RDKit::MolDraw2DJS... Generating docs for compound RDKit::MolDraw2DQt... Generating docs for compound RDKit::MolDraw2DSVG... Generating docs for compound RDKit::MolDraw2Dwx... Generating docs for compound RDKit::MolDrawOptions... Generating docs for compound RDKit::MolFileUnhandledFeatureException... Generating docs for compound RDKit::MolHolder... Generating docs for compound RDKit::MolHolderBase... Generating docs for compound RDKit::MolMatchFinalCheckFunctor... Generating docs for compound RDKit::MolPickler... Generating docs for compound RDKit::MolPicklerException... Generating docs for compound RDKit::MolSanitizeException... Generating docs for compound RDKit::MolSupplier... Generating docs for compound RDKit::MolWriter... Generating docs for compound RDKit::MolzipParams... Generating docs for compound RDKit::MultiFPBReader... Generating docs for compound RDKit::PatternHolder... Generating docs for compound RDKit::PDBMolSupplier... Generating docs for compound RDKit::PDBWriter... Generating docs for compound RDKit::PeriodicTable... Generating docs for compound RDKit::QueryAtom... Generating docs for compound RDKit::QueryAtomIterator_... Generating docs for compound RDKit::QueryBond... Generating docs for compound RDKit::RandomSampleAllBBsStrategy... Generating docs for compound RDKit::RandomSampleStrategy... Generating docs for compound RDKit::RCore... Generating docs for compound RDKit::RDAny... Generating docs for compound RDKit::RDProps... Generating docs for compound RDKit::RDValue... Generating docs for compound RDKit::ReactionFingerprintParams... Generating docs for compound RDKit::ReactionPickler... Generating docs for compound RDKit::React/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Resonance.h:114: warning: argument 'numThreads' of command @param is not found in the argument list of RDKit::ResonanceMolSupplier::ResonanceMolSupplier(ROMol &mol, unsigned int flags=0, unsigned int maxStructs=1000) /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatchers.h:336: warning: argument 'matches' of command @param is not found in the argument list of RDKit::SmartsMatcher::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 101 in file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:101: warning: The following parameter of RDKit::SmartsMatcher::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/Abbreviations.h:104: warning: The following parameter of RDKit::Abbreviations::findApplicableAbbreviationMatches(const ROMol &mol, const std::vector< AbbreviationDefinition > &abbrevs, double maxCoverage=0.4) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintGenerator.h:129: warning: The following parameters of RDKit::AtomPair::AtomPairAtomEnv::getBitId(FingerprintArguments< OutputType > *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, const AdditionalOutput *AdditionalOutput, const bool hashResults=false, const std::uint64_t fpSize=0) const are not documented: parameter 'AdditionalOutput' parameter 'fpSize' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairs.h:95: warning: The following parameter of RDKit::AtomPairs::getHashedAtomPairFingerprint(const ROMol &mol, unsigned int nBits=2048, unsigned int minLength=1, unsigned int maxLength=maxPathLen - 1, const std::vector< std::uint32_t > *fromAtoms=nullptr, const std::vector< std::uint32_t > *ignoreAtoms=nullptr, const std::vector< std::uint32_t > *atomInvariants=nullptr, bool includeChirality=false, bool use2D=true, int confId=-1) is not documented: parameter 'confId' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintUtil.h:75: warning: The following parameter of RDKit::AtomPairs::getTopologicalTorsionCode(const std::vector< std::uint32_t > &atomCodes, bool includeChirality=false) is not documented: parameter 'includeChirality' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Canon.h:103: warning: The following parameters of RDKit::Canon::canonicalizeFragment(ROMol &mol, int atomIdx, std::vector< AtomColors > &colors, const std::vector< unsigned int > &ranks, MolStack &molStack, const boost::dynamic_bitset<> *bondsInPlay=nullptr, const std::vector< std::string > *bondSymbols=nullptr, bool doIsomericSmiles=false, bool doRandom=false) are not documented: parameter 'bondsInPlay' parameter 'bondSymbols' parameter 'doIsomericSmiles' parameter 'doRandom' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Chirality.h:131: warning: The following parameter of RDKit::Chirality::findPotentialStereo(ROMol &mol, bool cleanIt, bool flagPossible=true) is not documented: parameter 'flagPossible' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Chirality.h:179: warning: The following parameter of RDKit::Chirality::getTrigonalBipyramidalAxialBond(const Atom *center, int which=0) is not documented: parameter 'center' ionPicklerException... Generating docs for compound RDKit::RecursiveStructureQuery... Generating docs for compound RDKit::ResonanceMolSupplier... Generating docs for compound RDKit::ResonanceMolSupplierCallback... Generating docs for compound RDKit::RGroupData... Generating docs for compound RDKit::RGroupDecompData... Generating docs for nested compound RDKit::RGroupDecompData::UsedLabels... Generating docs for compound RDKit::RGroupDecomposition... Generating docs for compound RDKit::RGroupDecompositionChromosome... Generating docs for compound RDKit::RGroupDecompositionParameters... Generating docs for compound RDKit::RGroupDecompositionProcessResult... Generating docs for compound RDKit::RGroupGa... Generating docs for compound RDKit::RGroupMatch... Generating docs for compound RDKit::RGroupScorer... Generating docs for compound RDKit::RingInfo... Generating docs for compound RDKit::ROMol... Generating docs for compound RDKit::RWMol... Generating docs for compound RDKit::RxnSanitizeException... Generating docs for compound RDKit::SDMolSupplier... Generating docs for compound RDKit::SDWriter... Generating docs for compound RDKit::SLNParseException... Generating docs for compound RDKit::SmartsMatcher... Generating docs for compound RDKit::SmartsParserParams... Generating docs for compound RDKit::SmilesMolSupplier... Generating docs for compound RDKit::SmilesParseException... Generating docs for compound RDKit::SmilesParserParams... Generating docs for compound RDKit::SmilesWriteParams... Generating docs for compound RDKit::SmilesWriter... Generating docs for compound RDKit::Snapshot... Generating docs for compound RDKit::SparseIntVect... Generating docs for compound RDKit::StereoBondThresholds... Generating docs for compound RDKit::StereoGroup... Generating docs for compound RDKit::SubstanceGroup... Generating docs for nested compound RDKit::SubstanceGroup::AttachPoint... Generating docs for nested compound RDKit::SubstanceGroup::CState... Generating docs for compound RDKit::SubstanceGroupException... Generating docs for compound RDKit::SubstructLibrary... Generating docs for compound RDKit::SubstructMatchParameters... Generating docs for compound RDKit::TautomerPatternHolder... Generating docs for compound RDKit::TautomerQuery... Generating docs for compound RDKit::TDTMolSupplier... Generating docs for compound RDKit::TDTWriter... Generating docs for compound RDKit::Trajectory... Generating docs for compound RDKit::UnimplementedFPException... Generating docs for compound RDKit::UsedLabelMap... Generating docs for compound RDKit::VarianceDataForLabel... Generating docs for namespace RDKit::Abbreviations Generating docs for compound RDKit::Abbreviations::AbbreviationDefinition... Generating docs for compound RDKit::Abbreviations::AbbreviationMatch... Generating docs for namespace RDKit::Abbreviations::common_properties Generating docs for namespace RDKit::Abbreviations::Utils Generating docs for namespace RDKit::AtomPair Generating docs for compound RDKit::AtomPair::AtomPairArguments... Generating docs for compound RDKit::AtomPair::AtomPairAtomEnv... Generating docs for compound RDKit::AtomPair::AtomPairAtomInvGenerator... Generating docs for compound RDKit::AtomPair::AtomPairEnvGenerator... Generating docs for namespace RDKit::AtomPairs Generating docs for namespace RDKit::Canon Generating docs for compound RDKit::Canon::AtomCompareFunctor... Generating docs for compound RDKit::Canon::bondholder... Generating docs for compound RDKit::Canon::canon_atom... Generating docs for compound RDKit::Canon::ChiralAtomCompareFunctor... Generating docs for compound RDKit::Canon::MolStackElem... Generating docs for compound RDKit::Canon::MolStackUnion... Generating docs for compound RDKit::Canon::SpecialChiralityAtomCompareFunctor... Generating docs for compound RDKit::Canon::SpecialSymmetryAtomCompareFunctor... Generating docs for namespace RDKit::Canon::detail Generating docs for namespace RDKit::Chirality Generating docs for compound RDKit::Chirality::StereoInfo... Generating docs for namespace RDKit::CIPLabeler Generating docs fo/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Lipinski.h:45: warning: argument 'strict' of command @param is not found in the argument list of RDKit::Descriptors::calcNumRotatableBonds(const ROMol &mol, NumRotatableBondsOptions useStrictDefinition=Default) /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Lipinski.h:45: warning: The following parameter of RDKit::Descriptors::calcNumRotatableBonds(const ROMol &mol, NumRotatableBondsOptions useStrictDefinition=Default) is not documented: parameter 'useStrictDefinition' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/USRDescriptor.h:68: warning: The following parameter of RDKit::Descriptors::USRCAT(const ROMol &mol, std::vector< double > &descriptor, std::vector< std::vector< unsigned int > > &atomIds, int confId=-1) is not documented: parameter 'atomIds' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h:37: warning: The following parameter of RDKit::DGeomHelpers::setTopolBounds(const ROMol &mol, DistGeom::BoundsMatPtr mmat, bool set15bounds=true, bool scaleVDW=false, bool useMacrocycle14config=false, bool forceTransAmides=true) is not documented: parameter 'forceTransAmides' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatchers.h:98: warning: argument 'matches' of command @param is not found in the argument list of RDKit::FilterMatchOps::And::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 101 in file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:101: warning: The following parameter of RDKit::FilterMatchOps::And::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatchers.h:218: warning: argument 'matches' of command @param is not found in the argument list of RDKit::FilterMatchOps::Not::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 101 in file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:101: warning: The following parameter of RDKit::FilterMatchOps::Not::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatchers.h:161: warning: argument 'matches' of command @param is not found in the argument list of RDKit::FilterMatchOps::Or::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const inherited from member getMatches at line 101 in file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatcherBase.h:101: warning: The following parameter of RDKit::FilterMatchOps::Or::getMatches(const ROMol &mol, std::vector< FilterMatch > &matchVect) const is not documented: parameter 'matchVect' r compound RDKit::CIPLabeler::CIPMol... Generating docs for compound RDKit::CIPLabeler::CIPMolSpan... Generating docs for nested compound RDKit::CIPLabeler::CIPMolSpan::CIPMolIter... Generating docs for compound RDKit::CIPLabeler::Configuration... Generating docs for compound RDKit::CIPLabeler::Digraph... Generating docs for compound RDKit::CIPLabeler::Edge... Generating docs for compound RDKit::CIPLabeler::Node... Generating docs for compound RDKit::CIPLabeler::PairList... Generating docs for compound RDKit::CIPLabeler::Priority... Generating docs for compound RDKit::CIPLabeler::Rule1a... Generating docs for compound RDKit::CIPLabeler::Rule1b... Generating docs for compound RDKit::CIPLabeler::Rule2... Generating docs for compound RDKit::CIPLabeler::Rule3... Generating docs for compound RDKit::CIPLabeler::Rule4a... Generating docs for compound RDKit::CIPLabeler::Rule4b... Generating docs for compound RDKit::CIPLabeler::Rule4c... Generating docs for compound RDKit::CIPLabeler::Rule5... Generating docs for compound RDKit::CIPLabeler::Rule5New... Generating docs for compound RDKit::CIPLabeler::Rule6... Generating docs for compound RDKit::CIPLabeler::Rules... Generating docs for compound RDKit::CIPLabeler::SequenceRule... Generating docs for compound RDKit::CIPLabeler::Sort... Generating docs for compound RDKit::CIPLabeler::Sp2Bond... Generating docs for compound RDKit::CIPLabeler::Tetrahedral... Generating docs for compound RDKit::CIPLabeler::TooManyNodesException... Generating docs for namespace RDKit::common_properties Generating docs for namespace RDKit::constants Generating docs for namespace RDKit::Deprotect Generating docs for compound RDKit::Deprotect::DeprotectData... Generating docs for namespace RDKit::Descriptors Generating docs for compound RDKit::Descriptors::CrippenParamCollection... Generating docs for compound RDKit::Descriptors::CrippenParams... Generating docs for compound RDKit::Descriptors::Properties... Generating docs for compound RDKit::Descriptors::PropertyFunctor... Generating docs for namespace RDKit::Descriptors::detail Generating docs for namespace RDKit::detail Generating docs for namespace RDKit::DGeomHelpers Generating docs for compound RDKit::DGeomHelpers::EmbedParameters... Generating docs for namespace RDKit::DTags Generating docs for namespace RDKit::EnumerationStrategyPickler Generating docs for namespace RDKit::EnumerationTypes Generating docs for namespace RDKit::FileParserUtils Generating docs for namespace RDKit::FilterMatchOps Generating docs for compound RDKit::FilterMatchOps::And... Generating docs for compound RDKit::FilterMatchOps::Not... Generating docs for compound RDKit::FilterMatchOps::Or... Generating docs for namespace RDKit::FMCS Generating docs for compound RDKit::FMCS::Composition2N... Generating docs for compound RDKit::FMCS::DuplicatedSeedCache... Generating docs for nested compound RDKit::FMCS::DuplicatedSeedCache::TKey... Generating docs for compound RDKit::FMCS::ExecStatistics... Generating docs for compound RDKit::FMCS::Graph... Generating docs for compound RDKit::FMCS::MaximumCommonSubgraph... Generating docs for compound RDKit::FMCS::MolFragment... Generating docs for compound RDKit::FMCS::NewBond... Generating docs for compound RDKit::FMCS::RingMatchTableSet... Generating docs for compound RDKit::FMCS::Seed... Generating docs for compound RDKit::FMCS::SeedSet... Generating docs for compound RDKit::FMCS::SubstructureCache... Generating docs for nested compound RDKit::FMCS::SubstructureCache::HashKey... Generating docs for nested compound RDKit::FMCS::SubstructureCache::KeyNumericMetrics... Generating docs for compound RDKit::FMCS::Target... Generating docs for compound RDKit::FMCS::TargetMatch... Generating docs for compound RDKit::FMCS::TArray2D... Generating docs for namespace RDKit::ForceFieldsHelper Generating docs for namespace RDKit::ForceFieldsHelper::detail Generating docs for namespace RDKit::GeneralMolSupplier Generating docs for compound RDKit::GeneralMolSupplier::SupplierOptions... Generating docs for namespace RDKit::GenericGroups Generating docs for/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MHFP.h:102: warning: found tag without matching /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MHFP.h:93: warning: The following parameter of RDKit::MHFPFingerprints::MHFPEncoder::CreateShingling(const ROMol &mol, unsigned char radius=3, bool rings=true, bool isomeric=false, bool kekulize=false, unsigned char min_radius=1) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MHFP.h:141: warning: found tag without matching /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MHFP.h:132: warning: The following parameter of RDKit::MHFPFingerprints::MHFPEncoder::Encode(ROMol &mol, unsigned char radius=3, bool rings=true, bool isomeric=false, bool kekulize=false, unsigned char min_radius=1) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MHFP.h:191: warning: found tag without matching /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MHFP.h:183: warning: The following parameter of RDKit::MHFPFingerprints::MHFPEncoder::EncodeSECFP(ROMol &mol, unsigned char radius=3, bool rings=true, bool isomeric=false, bool kekulize=false, unsigned char min_radius=1, size_t length=2048) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/MMPA.h:23: warning: The following parameter of RDKit::MMPA::fragmentMol(const ROMol &mol, std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR > > &result, unsigned int maxCuts=3, unsigned int maxCutBonds=20, const std::string &pattern="[#6+0;!$(*=,#[!#6])]!@!=!#[*]") is not documented: parameter 'pattern' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/MMPA.h:44: warning: The following parameter of RDKit::MMPA::fragmentMol(const ROMol &mol, std::vector< std::pair< ROMOL_SPTR, ROMOL_SPTR > > &result, unsigned int minCuts, unsigned int maxCuts, unsigned int maxCutBonds, const std::string &pattern="[#6+0;!$(*=,#[!#6])]!@!=!#[*]") is not documented: parameter 'pattern' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/AlignMolecules.h:147: warning: argument 'trans' of command @param is not found in the argument list of RDKit::MolAlign::getBestRMS(ROMol &prbMol, const ROMol &refMol, int prbCid=-1, int refCid=-1, const std::vector< MatchVectType > &map=std::vector< MatchVectType >(), int maxMatches=1e6, bool symmetrizeConjugatedTerminalGroups=true, const RDNumeric::DoubleVector *weights=nullptr) /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/AtomSymbol.h:39: warning: The following parameters of RDKit::MolDraw2D_detail::AtomSymbol::AtomSymbol(const std::string &symbol, int atIdx, OrientType orient, const Point2D &cds, const DrawColour &colour, DrawText &textDrawer) are not documented: parameter 'atIdx' parameter 'cds' parameter 'colour' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawMol.h:45: warning: argument 'highlightRadii' of command @param is not found in the argument list of RDKit::MolDraw2D_detail::DrawMol::DrawMol(const ROMol &mol, const std::string &legend, int width, int height, const MolDrawOptions &drawOptions, DrawText &textDrawer, const std::vector< int > *highlightAtoms=nullptr, const std::vector< int > *highlightBonds=nullptr, const std::map< int, DrawColour > *highlightAtomMap=nullptr, const std::map< int, DrawColour > *highlightBondMap=nullptr, const std::vector< std::pair< DrawColour, DrawColour > > *bondColours=nullptr, const std::map< int, double > *highlight_radii=nullptr, bool includeAnnotations=true, int confId=-1, bool isReactionMol=false) /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawMol.h:45: warning: The following parameters of RDKit::MolDraw2D_detail::DrawMol::DrawMol(const ROMol &mol, const std::string &legend, int width, int height, const MolDrawOptions &drawOptions, DrawText &textDrawer, const std::vector< int > *highlightAtoms=nullptr, const std::vector< int > *highlightBonds=nullptr, const std::map< int, DrawColour > *highlightAtomMap=nullptr, const std::map< int, DrawColour > *highlightBondMap=nullptr, const std::vector< std::pair< DrawColour, DrawColour > > *bondColours=nullptr, const std::map< int, double > *highlight_radii=nullptr, bool includeAnnotations=true, int confId=-1, bool isReactionMol=false) are not documented: parameter 'bondColours' parameter 'highlight_radii' parameter 'includeAnnotations' parameter 'isReactionMol' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawMolMCH.h:28: warning: argument 'highlightRadii' of command @param is not found in the argument list of RDKit::MolDraw2D_detail::DrawMolMCH::DrawMolMCH(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawMolMCH.h:28: warning: The following parameter of RDKit::MolDraw2D_detail::DrawMolMCH::DrawMolMCH(const ROMol &mol, const std::string &legend, int width, int height, MolDrawOptions &drawOptions, DrawText &textDrawer, const std::map< int, std::vector< DrawColour > > &highlight_atom_map, const std::map< int, std::vector< DrawColour > > &highlight_bond_map, const std::map< int, double > &highlight_radii, const std::map< int, int > &highlight_linewidth_multipliers, int confId=-1) is not documented: parameter 'highlight_radii' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:256: warning: The following parameter of RDKit::MolEnumerator::enumerate(const ROMol &mol, size_t maxPerOperation=0) is not documented: parameter 'mol' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:131: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:134: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:138: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:141: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:141: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:131: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:138: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:134: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:76: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:79: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:83: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:86: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:86: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:76: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:83: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:79: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:200: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:203: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:207: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:210: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:210: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:200: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:207: warning: Found unknown command '\override' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:203: warning: Found unknown command '\override' namespace RDKit::GenericGroups::Matchers Generating docs for namespace RDKit::Local Generating docs for namespace RDKit::MACCSFingerprints Generating docs for namespace RDKit::MHFPFingerprints Generating docs for compound RDKit::MHFPFingerprints::MHFPEncoder... Generating docs for namespace RDKit::MHFPFingerprints::FNV Generating docs for namespace RDKit::MMFF Generating docs for compound RDKit::MMFF::MMFFAtomProperties... Generating docs for compound RDKit::MMFF::MMFFMolProperties... Generating docs for namespace RDKit::MMFF::DefaultParameters Generating docs for namespace RDKit::MMFF::Tools Generating docs for compound RDKit::MMFF::Tools::DefaultTorsionBondSmarts... Generating docs for namespace RDKit::MMPA Generating docs for namespace RDKit::MolAlign Generating docs for compound RDKit::MolAlign::LAP... Generating docs for compound RDKit::MolAlign::MolAlignException... Generating docs for compound RDKit::MolAlign::MolHistogram... Generating docs for compound RDKit::MolAlign::O3A... Generating docs for compound RDKit::MolAlign::O3AConstraint... Generating docs for compound RDKit::MolAlign::O3AConstraintVect... Generating docs for compound RDKit::MolAlign::O3AFuncData... Generating docs for compound RDKit::MolAlign::SDM... Generating docs for namespace RDKit::MolDraw2D_detail Generating docs for compound RDKit::MolDraw2D_detail::AtomSymbol... Generating docs for compound RDKit::MolDraw2D_detail::DrawAnnotation... Generating docs for compound RDKit::MolDraw2D_detail::DrawMol... Generating docs for compound RDKit::MolDraw2D_detail::DrawMolMCH... Generating docs for compound RDKit::MolDraw2D_detail::DrawShape... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeArc... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeArrow... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeDashedWedge... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeEllipse... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapePolyLine... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeSimpleLine... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeSolidWedge... Generating docs for compound RDKit::MolDraw2D_detail::DrawShapeWavyLine... Generating docs for compound RDKit::MolDraw2D_detail::DrawText... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextCairo... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextFT... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextFTCairo... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextFTJS... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextFTQt... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextFTSVG... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextJS... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextNotFT... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextQt... Generating docs for compound RDKit::MolDraw2D_detail::DrawTextSVG... Generating docs for compound RDKit::MolDraw2D_detail::StringRect... Generating docs for namespace RDKit::MolDraw2DUtils Generating docs for compound RDKit::MolDraw2DUtils::ContourParams... Generating docs for namespace RDKit::MolEnumerator Generating docs for compound RDKit::MolEnumerator::LinkNode... Generating docs for compound RDKit::MolEnumerator::LinkNodeOp... Generating docs for compound RDKit::MolEnumerator::MolEnumeratorOp... Generating docs for compound RDKit::MolEnumerator::MolEnumeratorParams... Generating docs for compound RDKit::MolEnumerator::PositionVariationOp... Generating docs for compound RDKit::MolEnumerator::RepeatUnitOp... Generating docs for namespace RDKit::MolEnumerator::detail Generating docs for namespace RDKit::MolEnumerator::utils Generating docs for namespace RDKit::MolFragmenter Generating docs for compound RDKit::MolFragmenter::FragmenterBondType... Generating docs for namespace RDKit::MolHash Generating docs for namespace RDKit::MolInterchange Generating docs for compound RDKit::MolInterchange::JSONParseParameters... Generating docs for namespac/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolOps.h:762: warning: The following parameter of RDKit::MolOps::getAdjacencyMatrix(const ROMol &mol, bool useBO=false, int emptyVal=0, bool force=false, const char *propNamePrefix=nullptr, const boost::dynamic_bitset<> *bondsToUse=nullptr) is not documented: parameter 'bondsToUse' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolOps.h:281: warning: The following parameters of RDKit::MolOps::mergeQueryHs(const ROMol &mol, bool mergeUnmappedOnly=false, bool mergeIsotopes=false) are not documented: parameter 'mergeUnmappedOnly' parameter 'mergeIsotopes' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganGenerator.h:195: warning: argument 'countSimulation' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganGenerator.h:195: warning: argument 'includeChirality' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganGenerator.h:195: warning: argument 'onlyNonzeroInvariants' from the argument list of RDKit::MorganFingerprint::getMorganGenerator has multiple @param documentation sections /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintGenerator.h:129: warning: The following parameters of RDKit::MorganFingerprint::MorganAtomEnv::getBitId(FingerprintArguments< OutputType > *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, const AdditionalOutput *AdditionalOutput, const bool hashResults=false, const std::uint64_t fpSize=0) const are not documented: parameter 'AdditionalOutput' parameter 'fpSize' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganFingerprints.h:115: warning: The following parameter of RDKit::MorganFingerprints::getHashedFingerprint(const ROMol &mol, unsigned int radius, unsigned int nBits=2048, std::vector< boost::uint32_t > *invariants=nullptr, const std::vector< boost::uint32_t > *fromAtoms=nullptr, bool useChirality=false, bool useBondTypes=true, bool onlyNonzeroInvariants=false, BitInfoMap *atomsSettingBits=nullptr, bool includeRedundantEnvironments=false) is not documented: parameter 'nBits' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintGenerator.h:129: warning: The following parameters of RDKit::RDKitFP::RDKitFPAtomEnv::getBitId(FingerprintArguments< OutputType > *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, const AdditionalOutput *AdditionalOutput, bool hashResults=false, const std::uint64_t fpSize=0) const are not documented: parameter 'AdditionalOutput' parameter 'fpSize' e RDKit::MolOps Generating docs for compound RDKit::MolOps::AdjustQueryParameters... Generating docs for compound RDKit::MolOps::RemoveHsParameters... Generating docs for namespace RDKit::MolOps::details Generating docs for namespace RDKit::MolShapes Generating docs for namespace RDKit::MolStandardize Generating docs for compound RDKit::MolStandardize::AcidBaseCatalogEntry... Generating docs for compound RDKit::MolStandardize::AcidBaseCatalogParams... Generating docs for compound RDKit::MolStandardize::AllowedAtomsValidation... Generating docs for compound RDKit::MolStandardize::ChargeCorrection... Generating docs for compound RDKit::MolStandardize::CleanupParameters... Generating docs for compound RDKit::MolStandardize::DisallowedAtomsValidation... Generating docs for compound RDKit::MolStandardize::FragmentCatalogEntry... Generating docs for compound RDKit::MolStandardize::FragmentCatalogParams... Generating docs for compound RDKit::MolStandardize::FragmentRemover... Generating docs for compound RDKit::MolStandardize::FragmentValidation... Generating docs for compound RDKit::MolStandardize::IsotopeValidation... Generating docs for compound RDKit::MolStandardize::LargestFragmentChooser... Generating docs for nested compound RDKit::MolStandardize::LargestFragmentChooser::Largest... Generating docs for compound RDKit::MolStandardize::MetalDisconnector... Generating docs for compound RDKit::MolStandardize::MolVSValidation... Generating docs for compound RDKit::MolStandardize::MolVSValidations... Generating docs for compound RDKit::MolStandardize::NeutralValidation... Generating docs for compound RDKit::MolStandardize::NoAtomValidation... Generating docs for compound RDKit::MolStandardize::Normalizer... Generating docs for compound RDKit::MolStandardize::RDKitValidation... Generating docs for compound RDKit::MolStandardize::Reionizer... Generating docs for compound RDKit::MolStandardize::Tautomer... Generating docs for compound RDKit::MolStandardize::TautomerCatalogEntry... Generating docs for compound RDKit::MolStandardize::TautomerCatalogParams... Generating docs for compound RDKit::MolStandardize::TautomerEnumerator... Generating docs for compound RDKit::MolStandardize::TautomerEnumeratorCallback... Generating docs for compound RDKit::MolStandardize::TautomerEnumeratorResult... Generating docs for nested compound RDKit::MolStandardize::TautomerEnumeratorResult::const_iterator... Generating docs for compound RDKit::MolStandardize::TautomerTransform... Generating docs for compound RDKit::MolStandardize::TransformCatalogEntry... Generating docs for compound RDKit::MolStandardize::TransformCatalogParams... Generating docs for compound RDKit::MolStandardize::Uncharger... Generating docs for compound RDKit::MolStandardize::ValidationErrorInfo... Generating docs for compound RDKit::MolStandardize::ValidationMethod... Generating docs for namespace RDKit::MolStandardize::defaults Generating docs for namespace RDKit::MolStandardize::TautomerScoringFunctions Generating docs for namespace RDKit::MorganFingerprint Generating docs for compound RDKit::MorganFingerprint::MorganArguments... Generating docs for compound RDKit::MorganFingerprint::MorganAtomEnv... Generating docs for compound RDKit::MorganFingerprint::MorganAtomInvGenerator... Generating docs for compound RDKit::MorganFingerprint::MorganBondInvGenerator... Generating docs for compound RDKit::MorganFingerprint::MorganEnvGenerator... Generating docs for compound RDKit::MorganFingerprint::MorganFeatureAtomInvGenerator... Generating docs for namespace RDKit::MorganFingerprints Generating docs for compound RDKit::MorganFingerprints::ss_matcher... Generating docs for namespace RDKit::PicklerOps Generating docs for namespace RDKit::PNGData Generating docs for namespace RDKit::QueryOps Generating docs for namespace RDKit::RDKitFP Generating docs for compound RDKit::RDKitFP::RDKitFPArguments... Generating docs for compound RDKit::RDKitFP::RDKitFPAtomEnv... Generating docs for compound RDKit::RDKitFP::RDKitFPAtomInvGenerator... Generating docs for compound RDKit::RDKitFP::RDKitFPEnvG/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/ReducedGraphs.h:26: warning: The following parameter of RDKit::ReducedGraphs::generateMolExtendedReducedGraph(const ROMol &mol, std::vector< boost::dynamic_bitset<> > *atomTypes=nullptr) is not documented: parameter 'atomTypes' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/SanitizeRxn.h:127: warning: argument 'operationThatFailed' of command @param is not found in the argument list of RDKit::RxnOps::sanitizeRxn(ChemicalReaction &rxn, unsigned int &operationsThatFailed, unsigned int sanitizeOps=SANITIZE_ALL, const MolOps::AdjustQueryParameters ¶ms=DefaultRxnAdjustParams()) /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/SanitizeRxn.h:127: warning: The following parameters of RDKit::RxnOps::sanitizeRxn(ChemicalReaction &rxn, unsigned int &operationsThatFailed, unsigned int sanitizeOps=SANITIZE_ALL, const MolOps::AdjustQueryParameters ¶ms=DefaultRxnAdjustParams()) are not documented: parameter 'operationsThatFailed' parameter 'params' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:92: warning: argument 'useCountSimulation' of command @param is not found in the argument list of RDKit::TopologicalTorsion::getTopologicalTorsionGenerator(const bool includeChirality=false, const uint32_t torsionAtomCount=4, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, const bool countSimulation=true, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const std::uint32_t fpSize=2048, const bool ownsAtomInvGen=false) /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:92: warning: The following parameter of RDKit::TopologicalTorsion::getTopologicalTorsionGenerator(const bool includeChirality=false, const uint32_t torsionAtomCount=4, AtomInvariantsGenerator *atomInvariantsGenerator=nullptr, const bool countSimulation=true, const std::vector< std::uint32_t > countBounds={1, 2, 4, 8}, const std::uint32_t fpSize=2048, const bool ownsAtomInvGen=false) is not documented: parameter 'countSimulation' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:35: warning: argument 'useCountSimulation' of command @param is not found in the argument list of RDKit::TopologicalTorsion::TopologicalTorsionArguments< OutputType >::TopologicalTorsionArguments(const bool includeChirality, const uint32_t torsionAtomCount, const bool countSimulation, const std::vector< std::uint32_t > countBounds, const std::uint32_t fpSize) /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:35: warning: The following parameter of RDKit::TopologicalTorsion::TopologicalTorsionArguments::TopologicalTorsionArguments(const bool includeChirality, const uint32_t torsionAtomCount, const bool countSimulation, const std::vector< std::uint32_t > countBounds, const std::uint32_t fpSize) is not documented: parameter 'countSimulation' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:67: warning: The following parameter of RDKit::TopologicalTorsion::TopologicalTorsionAtomEnv::TopologicalTorsionAtomEnv(OutputType bitId, INT_VECT atomPath) is not documented: parameter 'atomPath' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintGenerator.h:129: warning: The following parameters of RDKit::TopologicalTorsion::TopologicalTorsionAtomEnv::getBitId(FingerprintArguments< OutputType > *arguments, const std::vector< std::uint32_t > *atomInvariants, const std::vector< std::uint32_t > *bondInvariants, const AdditionalOutput *AdditionalOutput, const bool hashResults=false, const std::uint64_t fpSize=0) const are not documented: parameter 'AdditionalOutput' parameter 'fpSize' /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/HierarchicalClusterPicker.h:48: warning: The following parameter of RDPickers::HierarchicalClusterPicker::pick(const double *distMat, unsigned int poolSize, unsigned int pickSize) const is not documented: parameter 'distMat' /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/LeaderPicker.h:48: warning: argument 'firstPicks' of command @param is not found in the argument list of RDPickers::LeaderPicker::lazyPick(T &func, unsigned int poolSize, unsigned int pickSize) const /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/LeaderPicker.h:48: warning: argument 'seed' of command @param is not found in the argument list of RDPickers::LeaderPicker::lazyPick(T &func, unsigned int poolSize, unsigned int pickSize) const /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/LeaderPicker.h:87: warning: The following parameters of RDPickers::LeaderPicker::pick(const double *distMat, unsigned int poolSize, unsigned int pickSize, const RDKit::INT_VECT &firstPicks, double threshold, int nthreads) const are not documented: parameter 'threshold' parameter 'nthreads' /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/MaxMinPicker.h:44: warning: argument 'firstPicks' of command @param is not found in the argument list of RDPickers::MaxMinPicker::lazyPick(T &func, unsigned int poolSize, unsigned int pickSize) const /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/MaxMinPicker.h:44: warning: argument 'seed' of command @param is not found in the argument list of RDPickers::MaxMinPicker::lazyPick(T &func, unsigned int poolSize, unsigned int pickSize) const enerator... Generating docs for namespace RDKit::RDKitFPUtils Generating docs for namespace RDKit::RDTypeTag Generating docs for namespace RDKit::RDTypeTag::detail Generating docs for compound RDKit::RDTypeTag::detail::Value... Generating docs for namespace RDKit::ReactionRunnerUtils Generating docs for namespace RDKit::ReducedGraphs Generating docs for namespace RDKit::RxnOps Generating docs for namespace RDKit::ScaffoldNetwork Generating docs for compound RDKit::ScaffoldNetwork::NetworkEdge... Generating docs for compound RDKit::ScaffoldNetwork::ScaffoldNetwork... Generating docs for compound RDKit::ScaffoldNetwork::ScaffoldNetworkParams... Generating docs for namespace RDKit::ScaffoldNetwork::detail Generating docs for namespace RDKit::SGroupParsing Generating docs for namespace RDKit::SGroupWriting Generating docs for namespace RDKit::SLNParse Generating docs for compound RDKit::SLNParse::AttribType... Generating docs for namespace RDKit::SmartsWrite Generating docs for namespace RDKit::SmilesWrite Generating docs for namespace RDKit::StructureCheck Generating docs for compound RDKit::StructureCheck::AugmentedAtom... Generating docs for compound RDKit::StructureCheck::ChargeFix... Generating docs for compound RDKit::StructureCheck::IncEntry... Generating docs for compound RDKit::StructureCheck::Ligand... Generating docs for compound RDKit::StructureCheck::Neighbourhood... Generating docs for compound RDKit::StructureCheck::PathEntry... Generating docs for compound RDKit::StructureCheck::StructChecker... Generating docs for compound RDKit::StructureCheck::StructCheckerOptions... Generating docs for compound RDKit::StructureCheck::StructCheckTautomer... Generating docs for namespace RDKit::Subgraphs Generating docs for namespace RDKit::SubstanceGroupChecks Generating docs for namespace RDKit::TopologicalTorsion Generating docs for compound RDKit::TopologicalTorsion::TopologicalTorsionArguments... Generating docs for compound RDKit::TopologicalTorsion::TopologicalTorsionAtomEnv... Generating docs for compound RDKit::TopologicalTorsion::TopologicalTorsionEnvGenerator... Generating docs for namespace RDKit::UFF Generating docs for namespace RDKit::UFF::Tools Generating docs for compound RDKit::UFF::Tools::DefaultTorsionBondSmarts... Generating docs for namespace RDKit::Utils Generating docs for compound RDKit::Utils::LocaleSwitcher... Generating docs for namespace RDKit::Utils::detail Generating docs for namespace RDLog Generating docs for compound RDLog::LogStateSetter... Generating docs for namespace RDNumeric Generating docs for compound RDNumeric::Matrix... Generating docs for compound RDNumeric::SquareMatrix... Generating docs for compound RDNumeric::SymmMatrix... Generating docs for compound RDNumeric::Vector... Generating docs for namespace RDNumeric::Alignments Generating docs for namespace RDNumeric::EigenSolvers Generating docs for namespace RDPickers Generating docs for compound RDPickers::DistPicker... Generating docs for compound RDPickers::HierarchicalClusterPicker... Generating docs for compound RDPickers::LeaderPicker... Generating docs for compound RDPickers::LeaderPickerState... Generating docs for compound RDPickers::MaxMinPicker... Generating docs for compound RDPickers::MaxMinPickInfo... Generating docs for namespace RingUtils Generating docs for namespace SmilesParseOps Generating docs for namespace SmilesParseOps::detail Generating graph info page... Generating directory documentation... Generating index page... Generating page index... Generating module index... Generating namespace index... Generating namespace member index... Generating concept index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Running plantuml with JAVA... lookup cache used 20179/65536 hits=157801 misses=23544 finished... (cd /build/reproducible-path/rdkit-202209.3/Docs/Book; RDBASE=/build/reproducible-path/rdkit-202209.3 /usr/bin/make html) make[2]: Entering directory '/build/reproducible-path/rdkit-202209.3/Docs/Book' mkdir -p _build/html/cppapi cp -r /build/reproducible-path/rdkit-202209.3/Code/docs/* _build/html/cppapi cp -r C++Examples _build/html/ sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v5.3.0 WARNING: html_static_path entry '_static' does not exist building [mo]: targets for 0 po files that are out of date building [html]: targets for 306 source files that are out of date updating environment: [new config] 306 added, 0 changed, 0 removed reading sources... [ 0%] BackwardsIncompatibleChanges /usr/lib/python3/dist-packages/recommonmark/parser.py:75: UserWarning: Container node skipped: type=document warn("Container node skipped: type={0}".format(mdnode.t)) reading sources... 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/build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInPython.rst:421: WARNING: duplicate label working with molecules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInPython.rst:425: WARNING: duplicate label looping over atoms and bonds, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInPython.rst:468: WARNING: duplicate label ring information, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInPython.rst:537: WARNING: duplicate label modifying molecules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInPython.rst:605: WARNING: duplicate label working with 2d molecules: generating depictions, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInPython.rst:655: WARNING: duplicate label working with 3d molecules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInPython.rst:778: WARNING: duplicate label preserving molecules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInPython.rst:834: WARNING: duplicate label drawing molecules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInPython.rst:1071: WARNING: duplicate label substructure searching, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInPython.rst:1136: WARNING: duplicate label stereochemistry in substructure matches, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInPython.rst:1174: WARNING: duplicate label atom map indices in smarts, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInPython.rst:3407: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/Cartridge.md /build/reproducible-path/rdkit-202209.3/Docs/Book/Install.md:444: WARNING: duplicate label recommended extras, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/Install.md /build/reproducible-path/rdkit-202209.3/Docs/Book/Install.md:488: WARNING: duplicate label testing the build (optional, but recommended), other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/Install.md /build/reproducible-path/rdkit-202209.3/Docs/Book/Install.md:493: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInPython.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/Overview.md:143: WARNING: duplicate label footnotes, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInC++.md /build/reproducible-path/rdkit-202209.3/Docs/Book/Overview.md:148: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/Install.md /build/reproducible-path/rdkit-202209.3/Docs/Book/RDKit_Book.rst:180: WARNING: duplicate label aromaticity, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/RDKit_Book.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/RDKit_Book.rst:385: WARNING: duplicate label dative bonds, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/RDKit_Book.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/RDKit_Book.rst:1262: WARNING: duplicate label chemical features, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInPython.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/RDKit_Book.rst:2109: WARNING: duplicate label introduction, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/Cartridge.md /build/reproducible-path/rdkit-202209.3/Docs/Book/RDKit_Book.rst:2373: WARNING: duplicate label license, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/Overview.md /build/reproducible-path/rdkit-202209.3/Docs/Book/index.rst:9: WARNING: toctree contains reference to nonexisting document 'Cookbook' WARNING: autodoc: failed to import module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Avalon' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Avalon.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Avalon.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.rst WARNING: autodoc: failed to import module 'Avalon.pyAvalonTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rst:30: WARNING: toctree contains reference to nonexisting document 'source/rdkit.Chem.DSViewer' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rst:30: WARNING: toctree contains reference to nonexisting document 'source/rdkit.Chem.rdStructChecker' WARNING: autodoc: failed to import module 'Chem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rst:28: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Avalon.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rst:114: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Avalon.rst WARNING: autodoc: failed to import module 'Chem.AllChem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.AtomPairs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.AtomPairs.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rst WARNING: autodoc: failed to import module 'Chem.AtomPairs.Pairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Sheridan' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Torsions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.BRICS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.BuildFragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.ChemUtils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.AtomPairs.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.ChemUtils.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.AtomPairs.rst WARNING: autodoc: failed to import module 'Chem.ChemUtils.AlignDepict' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.BulkTester' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.DescriptorUtilities' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.SDFToCSV' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.TemplateExpand' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemicalForceFields' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Crippen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Descriptors3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Draw.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.ChemUtils.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Draw.rst:21: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.ChemUtils.rst WARNING: autodoc: failed to import module 'Chem.Draw.IPythonConsole' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.MolDrawing' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.SimilarityMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.aggCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.cairoCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.canvasbase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.mplCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.qtCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2DQt' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.EState.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Draw.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.EState.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Draw.rst WARNING: autodoc: failed to import module 'Chem.EState.AtomTypes' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.EState_VSA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.Fingerprinter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EnumerateHeterocycles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EnumerateStereoisomers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FastSDMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatFinderCLI' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.FeatMaps.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.EState.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.FeatMaps.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.EState.rst WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapParser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapPoint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Features' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Features.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.FeatMaps.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Features.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.FeatMaps.rst WARNING: autodoc: failed to import module 'Chem.Features.FeatDirUtilsRD' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Features.ShowFeats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FilterCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Fingerprints.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Features.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Fingerprints.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Features.rst WARNING: autodoc: failed to import module 'Chem.Fingerprints.ClusterMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.DbFpSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.FingerprintMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.MolSimilarity' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.SimilarityScreener' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fraggle' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Fraggle.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Fingerprints.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Fraggle.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Fingerprints.rst WARNING: autodoc: failed to import module 'Chem.Fraggle.FraggleSim' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FragmentMatcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fragments' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FunctionalGroups' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.GraphDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Graphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Lipinski' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MACCSkeys' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MCS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.MolDb.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Fraggle.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.MolDb.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Fraggle.rst WARNING: autodoc: failed to import module 'Chem.MolDb.FingerprintUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.Loader' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_orig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_sa' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.MolKey.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.MolDb.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.MolKey.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.MolDb.rst WARNING: autodoc: failed to import module 'Chem.MolKey.InchiInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolKey.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.MolStandardize.rst:6: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.MolKey.rst WARNING: autodoc: failed to import module 'Chem.MolStandardize.rdMolStandardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolSurf' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PandasTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PeriodicTable' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Pharm2D.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.MolStandardize.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Pharm2D.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.MolKey.rst WARNING: autodoc: failed to import module 'Chem.Pharm2D.Generate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Gobbi_Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Matcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.SigFactory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Pharm3D.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Pharm2D.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Pharm3D.rst:14: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Pharm2D.rst WARNING: autodoc: failed to import module 'Chem.Pharm3D.EmbedLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D.ExcludedVolume' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D.Pharmacophore' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PropertyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.QED' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Randomize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Recap' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.RegistrationHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SATIS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SaltRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Scaffolds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Scaffolds.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Pharm3D.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Scaffolds.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Pharm3D.rst WARNING: autodoc: failed to import module 'Chem.Scaffolds.MurckoScaffold' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Scaffolds.rdScaffoldNetwork' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ShowMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SimpleEnum' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.SimpleEnum.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Scaffolds.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.SimpleEnum.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Scaffolds.rst WARNING: autodoc: failed to import module 'Chem.SimpleEnum.Enumerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Subshape.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.SimpleEnum.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Subshape.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.SimpleEnum.rst WARNING: autodoc: failed to import module 'Chem.Subshape.BuilderUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeAligner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeBuilder' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeObjects' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Suppliers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Suppliers.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Subshape.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Suppliers.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Subshape.rst WARNING: autodoc: failed to import module 'Chem.Suppliers.DbMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Suppliers.MolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.TemplateAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.TorsionFingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.fmcs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Suppliers.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.fmcs.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Suppliers.rst WARNING: autodoc: failed to import module 'Chem.fmcs.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.inchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdAbbreviations' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdCIPLabeler' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdChemReactions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rdChemicalFeatures.rst:2: WARNING: Title underline too short. rdkit.Chem.rdChemicalFeatures module ================================= WARNING: autodoc: failed to import module 'Chem.rdChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdCoordGen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdDepictor' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdDeprotect' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdDistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdEHTTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdFMCS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdFingerprintGenerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rdForceFieldHelpers.rst:2: WARNING: Title underline too short. rdkit.Chem.rdForceFieldHelpers module ================================= WARNING: autodoc: failed to import module 'Chem.rdForceFieldHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdFreeSASA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMHFPFingerprint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMMPA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rdMolChemicalFeatures.rst:2: WARNING: Title underline too short. rdkit.Chem.rdMolChemicalFeatures module ================================= WARNING: autodoc: failed to import module 'Chem.rdMolChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rdMolDescriptors.rst:2: WARNING: Title underline too short. rdkit.Chem.rdMolDescriptors module ================================= WARNING: autodoc: failed to import module 'Chem.rdMolDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolEnumerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rdMolInterchange.rst:2: WARNING: Title underline too short. rdkit.Chem.rdMolInterchange module ================================= WARNING: autodoc: failed to import module 'Chem.rdMolInterchange' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolTransforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rdPartialCharges.rst:2: WARNING: Title underline too short. rdkit.Chem.rdPartialCharges module ================================= WARNING: autodoc: failed to import module 'Chem.rdPartialCharges' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rdRGroupDecomposition.rst:2: WARNING: Title underline too short. rdkit.Chem.rdRGroupDecomposition module ================================= WARNING: autodoc: failed to import module 'Chem.rdRGroupDecomposition' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdSLNParse' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdShapeHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rdSubstructLibrary.rst:2: WARNING: Title underline too short. rdkit.Chem.rdSubstructLibrary module ================================= WARNING: autodoc: failed to import module 'Chem.rdSubstructLibrary' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdTautomerQuery' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdchem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdfiltercatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdfragcatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdinchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdmolfiles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdmolops' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdqueries' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdtrajectory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataManip' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DataManip.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DataManip.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.fmcs.rst WARNING: autodoc: failed to import module 'DataManip.Metric' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DataManip.Metric.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.fmcs.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DataManip.Metric.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DataManip.rst WARNING: autodoc: failed to import module 'DataManip.Metric.rdMetricMatrixCalc' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DataStructs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DataManip.Metric.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DataStructs.rst:18: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DataManip.Metric.rst WARNING: autodoc: failed to import module 'DataStructs.BitEnsemble' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.BitEnsembleDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.BitUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.LazySignature' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.TopNContainer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.VectCollection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.cDataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Dbase.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DataStructs.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Dbase.rst:18: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DataStructs.rst WARNING: autodoc: failed to import module 'Dbase.DbConnection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbModule' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbReport' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbResultSet' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.StorageUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DistanceGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DistanceGeometry.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Dbase.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DistanceGeometry.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Dbase.rst WARNING: autodoc: failed to import module 'DistanceGeometry.DistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ForceField.rst:5: WARNING: Block quote ends without a blank line; unexpected unindent. WARNING: autodoc: failed to import module 'ForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ForceField.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DistanceGeometry.rst WARNING: autodoc: failed to import module 'ForceField.rdForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Geometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Geometry.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DistanceGeometry.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Geometry.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ForceField.rst WARNING: autodoc: failed to import module 'Geometry.rdGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DataManip.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.rst:24: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Geometry.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.rst:38: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Geometry.rst WARNING: autodoc: failed to import module 'ML.AnalyzeComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.BuildComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Cluster.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Cluster.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.rst WARNING: autodoc: failed to import module 'ML.Cluster.Butina' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.ClusterUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.ClusterVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Clustering' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Clusters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Murtagh' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Resemblance' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Standardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Composite.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Cluster.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Composite.rst:14: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Cluster.rst WARNING: autodoc: failed to import module 'ML.Composite.AdjustComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite.BayesComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite.Composite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.CompositeRun' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Data.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Composite.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Data.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Composite.rst WARNING: autodoc: failed to import module 'ML.Data.DataUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.FindQuantBounds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.MLData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.Quantize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.SplitData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.Stats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.Transforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.cQuantize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.DecTree.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Data.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.DecTree.rst:23: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Data.rst WARNING: autodoc: failed to import module 'ML.DecTree.BuildQuantTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.BuildSigTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.DecTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.Forest' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.ID3' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.PruneTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.QuantTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.SigTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.Tree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.TreeUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.TreeVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Descriptors.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.DecTree.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Descriptors.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.DecTree.rst WARNING: autodoc: failed to import module 'ML.Descriptors.CompoundDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.MoleculeDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.Parser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.EnrichPlot' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.GrowComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.InfoTheory.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Descriptors.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.InfoTheory.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Descriptors.rst WARNING: autodoc: failed to import module 'ML.InfoTheory.BitClusterer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory.BitRank' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory.entropy' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.InfoTheory.rdInfoTheory.rst:2: WARNING: Title underline too short. rdkit.ML.InfoTheory.rdInfoTheory module ====================================== WARNING: autodoc: failed to import module 'ML.InfoTheory.rdInfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.KNN.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.InfoTheory.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.KNN.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.InfoTheory.rst WARNING: autodoc: failed to import module 'ML.KNN.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.DistFunctions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.KNNClassificationModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.KNNModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.KNNRegressionModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.MLUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.MLUtils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.KNN.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.MLUtils.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.KNN.rst WARNING: autodoc: failed to import module 'ML.MLUtils.VoteImg' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.MatOps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ModelPackage' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.ModelPackage.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.MLUtils.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.ModelPackage.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.MLUtils.rst WARNING: autodoc: failed to import module 'ML.ModelPackage.PackageUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ModelPackage.Packager' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.NaiveBayes' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.NaiveBayes.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.ModelPackage.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.NaiveBayes.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.ModelPackage.rst WARNING: autodoc: failed to import module 'ML.NaiveBayes.ClassificationModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.NaiveBayes.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Neural.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.NaiveBayes.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Neural.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.NaiveBayes.rst WARNING: autodoc: failed to import module 'ML.Neural.ActFuncs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.NetNode' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.Network' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.Trainers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.SLT' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.SLT.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Neural.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.SLT.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Neural.rst WARNING: autodoc: failed to import module 'ML.SLT.Risk' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Scoring.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.SLT.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Scoring.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.SLT.rst WARNING: autodoc: failed to import module 'ML.Scoring.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ScreenComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.files' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Numerics' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Numerics.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Scoring.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Numerics.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Scoring.rst WARNING: autodoc: failed to import module 'Numerics.rdAlignment' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDConfig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDLogger' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDPaths' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDRandom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'SimDivFilters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.SimDivFilters.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Numerics.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.SimDivFilters.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Numerics.rst WARNING: autodoc: failed to import module 'SimDivFilters.SimilarityPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'SimDivFilters.rdSimDivPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'TestRunner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.VLib.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.VLib.rst:12: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.SimDivFilters.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.VLib.rst:23: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.SimDivFilters.rst WARNING: autodoc: failed to import module 'VLib.Filter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Node' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.VLib.NodeLib.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.VLib.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.VLib.NodeLib.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.VLib.rst WARNING: autodoc: failed to import module 'VLib.NodeLib.DbMolSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.DbPickleSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SDSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsMolFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesDupeFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesOutput' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Output' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Supply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Transform' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'rdBase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'six' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.utils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.VLib.NodeLib.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.utils.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.VLib.NodeLib.rst WARNING: autodoc: failed to import module 'utils.cactvs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.chemutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.fileutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.listutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.spiral' from module 'rdkit'; the following exception was raised: No module named 'rdkit' looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/rdkit-202209.3/Docs/Book/data/README.md: WARNING: document isn't included in any toctree /build/reproducible-path/rdkit-202209.3/Docs/Book/source/modules.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 0%] BackwardsIncompatibleChanges writing output... [ 0%] Cartridge writing output... [ 0%] GettingStartedInC++ writing output... [ 1%] GettingStartedInPython writing output... [ 1%] Install writing output... [ 1%] Overview writing output... [ 2%] RDKit_Book writing output... [ 2%] api-docs writing output... [ 2%] data/README writing output... [ 3%] index writing output... [ 3%] source/modules writing output... [ 3%] source/rdkit writing output... [ 4%] source/rdkit.Avalon writing output... [ 4%] source/rdkit.Avalon.pyAvalonTools writing output... [ 4%] source/rdkit.Chem writing output... [ 5%] source/rdkit.Chem.AllChem writing output... [ 5%] source/rdkit.Chem.AtomPairs writing output... [ 5%] source/rdkit.Chem.AtomPairs.Pairs writing output... [ 6%] source/rdkit.Chem.AtomPairs.Sheridan writing output... [ 6%] source/rdkit.Chem.AtomPairs.Torsions writing output... [ 6%] source/rdkit.Chem.AtomPairs.Utils writing output... [ 7%] source/rdkit.Chem.BRICS writing output... [ 7%] source/rdkit.Chem.BuildFragmentCatalog writing output... [ 7%] source/rdkit.Chem.ChemUtils writing output... [ 8%] source/rdkit.Chem.ChemUtils.AlignDepict writing output... [ 8%] source/rdkit.Chem.ChemUtils.BulkTester writing output... [ 8%] source/rdkit.Chem.ChemUtils.DescriptorUtilities writing output... [ 9%] source/rdkit.Chem.ChemUtils.SDFToCSV writing output... [ 9%] source/rdkit.Chem.ChemUtils.TemplateExpand writing output... [ 9%] source/rdkit.Chem.ChemicalFeatures writing output... [ 10%] source/rdkit.Chem.ChemicalForceFields writing output... [ 10%] source/rdkit.Chem.Crippen writing output... [ 10%] source/rdkit.Chem.Descriptors writing output... [ 11%] source/rdkit.Chem.Descriptors3D writing output... [ 11%] source/rdkit.Chem.Draw writing output... [ 11%] source/rdkit.Chem.Draw.IPythonConsole writing output... [ 12%] source/rdkit.Chem.Draw.MolDrawing writing output... [ 12%] source/rdkit.Chem.Draw.SimilarityMaps writing output... [ 12%] source/rdkit.Chem.Draw.aggCanvas writing output... [ 13%] source/rdkit.Chem.Draw.cairoCanvas writing output... [ 13%] source/rdkit.Chem.Draw.canvasbase writing output... [ 13%] source/rdkit.Chem.Draw.mplCanvas writing output... [ 14%] source/rdkit.Chem.Draw.qtCanvas writing output... [ 14%] source/rdkit.Chem.Draw.rdMolDraw2D writing output... [ 14%] source/rdkit.Chem.Draw.rdMolDraw2DQt writing output... [ 15%] source/rdkit.Chem.EState writing output... [ 15%] source/rdkit.Chem.EState.AtomTypes writing output... [ 15%] source/rdkit.Chem.EState.EState writing output... [ 16%] source/rdkit.Chem.EState.EState_VSA writing output... [ 16%] source/rdkit.Chem.EState.Fingerprinter writing output... [ 16%] source/rdkit.Chem.EnumerateHeterocycles writing output... [ 16%] source/rdkit.Chem.EnumerateStereoisomers writing output... [ 17%] source/rdkit.Chem.FastSDMolSupplier writing output... [ 17%] source/rdkit.Chem.FeatFinderCLI writing output... 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[100%] source/rdkit.utils.spiral /build/reproducible-path/rdkit-202209.3/Docs/Book/index.rst:9: WARNING: toctree contains reference to nonexisting document 'Cookbook' WARNING: autodoc: failed to import module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.VLib.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.rst:24: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.utils.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.rst:37: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.utils.rst WARNING: autodoc: failed to import module 'Avalon' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Avalon.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Avalon.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.rst WARNING: autodoc: failed to import module 'Avalon.pyAvalonTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rst:30: WARNING: toctree contains reference to nonexisting document 'source/rdkit.Chem.DSViewer' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rst:30: WARNING: toctree contains reference to nonexisting document 'source/rdkit.Chem.rdStructChecker' WARNING: autodoc: failed to import module 'Chem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rst:28: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Avalon.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rst:114: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Avalon.rst WARNING: autodoc: failed to import module 'Chem.AllChem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.AtomPairs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.AtomPairs.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rst WARNING: autodoc: failed to import module 'Chem.AtomPairs.Pairs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Sheridan' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Torsions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.AtomPairs.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.BRICS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.BuildFragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.ChemUtils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.AtomPairs.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.ChemUtils.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.AtomPairs.rst WARNING: autodoc: failed to import module 'Chem.ChemUtils.AlignDepict' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.BulkTester' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.DescriptorUtilities' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.SDFToCSV' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemUtils.TemplateExpand' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ChemicalForceFields' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Crippen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Descriptors3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Draw.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.ChemUtils.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Draw.rst:21: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.ChemUtils.rst WARNING: autodoc: failed to import module 'Chem.Draw.IPythonConsole' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.MolDrawing' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.SimilarityMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.aggCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.cairoCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.canvasbase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.mplCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.qtCanvas' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Draw.rdMolDraw2DQt' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.EState.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Draw.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.EState.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Draw.rst WARNING: autodoc: failed to import module 'Chem.EState.AtomTypes' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.EState' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.EState_VSA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EState.Fingerprinter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EnumerateHeterocycles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.EnumerateStereoisomers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FastSDMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatFinderCLI' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.FeatMaps.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.EState.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.FeatMaps.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.EState.rst WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapParser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapPoint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMapUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FeatMaps.FeatMaps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Features' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Features.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.FeatMaps.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Features.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.FeatMaps.rst WARNING: autodoc: failed to import module 'Chem.Features.FeatDirUtilsRD' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Features.ShowFeats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FilterCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Fingerprints.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Features.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Fingerprints.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Features.rst WARNING: autodoc: failed to import module 'Chem.Fingerprints.ClusterMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.DbFpSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.FingerprintMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.MolSimilarity' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fingerprints.SimilarityScreener' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fraggle' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Fraggle.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Fingerprints.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Fraggle.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Fingerprints.rst WARNING: autodoc: failed to import module 'Chem.Fraggle.FraggleSim' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FragmentCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FragmentMatcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Fragments' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.FunctionalGroups' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.GraphDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Graphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Lipinski' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MACCSkeys' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MCS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.MolDb.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Fraggle.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.MolDb.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Fraggle.rst WARNING: autodoc: failed to import module 'Chem.MolDb.FingerprintUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.Loader' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_orig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolDb.Loader_sa' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.MolKey.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.MolDb.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.MolKey.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.MolDb.rst WARNING: autodoc: failed to import module 'Chem.MolKey.InchiInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolKey.MolKey' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolStandardize.rdMolStandardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.MolSurf' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PandasTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PeriodicTable' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Pharm2D.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.MolKey.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Pharm2D.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.MolKey.rst WARNING: autodoc: failed to import module 'Chem.Pharm2D.Generate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Gobbi_Pharm2D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Matcher' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.SigFactory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm2D.Utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Pharm3D.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Pharm2D.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Pharm3D.rst:14: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Pharm2D.rst WARNING: autodoc: failed to import module 'Chem.Pharm3D.EmbedLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D.ExcludedVolume' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Pharm3D.Pharmacophore' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PropertyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.PyMol' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.QED' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Randomize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Recap' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.RegistrationHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SATIS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SaltRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Scaffolds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Scaffolds.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Pharm3D.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Scaffolds.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Pharm3D.rst WARNING: autodoc: failed to import module 'Chem.Scaffolds.MurckoScaffold' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Scaffolds.rdScaffoldNetwork' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.ShowMols' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.SimpleEnum' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.SimpleEnum.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Scaffolds.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.SimpleEnum.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Scaffolds.rst WARNING: autodoc: failed to import module 'Chem.SimpleEnum.Enumerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Subshape.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.SimpleEnum.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Subshape.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.SimpleEnum.rst WARNING: autodoc: failed to import module 'Chem.Subshape.BuilderUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeAligner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeBuilder' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Subshape.SubshapeObjects' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Suppliers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Suppliers.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Subshape.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Suppliers.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Subshape.rst WARNING: autodoc: failed to import module 'Chem.Suppliers.DbMolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.Suppliers.MolSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.TemplateAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.TorsionFingerprints' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.fmcs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Suppliers.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.fmcs.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.Suppliers.rst WARNING: autodoc: failed to import module 'Chem.fmcs.fmcs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.inchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdAbbreviations' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdCIPLabeler' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdChemReactions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rdChemicalFeatures.rst:2: WARNING: Title underline too short. rdkit.Chem.rdChemicalFeatures module ================================= WARNING: autodoc: failed to import module 'Chem.rdChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdCoordGen' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdDepictor' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdDeprotect' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdDistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdEHTTools' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdFMCS' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdFingerprintGenerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rdForceFieldHelpers.rst:2: WARNING: Title underline too short. rdkit.Chem.rdForceFieldHelpers module ================================= WARNING: autodoc: failed to import module 'Chem.rdForceFieldHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdFreeSASA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMHFPFingerprint' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMMPA' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolAlign' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolCatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rdMolChemicalFeatures.rst:2: WARNING: Title underline too short. rdkit.Chem.rdMolChemicalFeatures module ================================= WARNING: autodoc: failed to import module 'Chem.rdMolChemicalFeatures' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rdMolDescriptors.rst:2: WARNING: Title underline too short. rdkit.Chem.rdMolDescriptors module ================================= WARNING: autodoc: failed to import module 'Chem.rdMolDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolEnumerator' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolHash' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rdMolInterchange.rst:2: WARNING: Title underline too short. rdkit.Chem.rdMolInterchange module ================================= WARNING: autodoc: failed to import module 'Chem.rdMolInterchange' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdMolTransforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rdPartialCharges.rst:2: WARNING: Title underline too short. rdkit.Chem.rdPartialCharges module ================================= WARNING: autodoc: failed to import module 'Chem.rdPartialCharges' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rdRGroupDecomposition.rst:2: WARNING: Title underline too short. rdkit.Chem.rdRGroupDecomposition module ================================= WARNING: autodoc: failed to import module 'Chem.rdRGroupDecomposition' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdReducedGraphs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdSLNParse' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdShapeHelpers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rdSubstructLibrary.rst:2: WARNING: Title underline too short. rdkit.Chem.rdSubstructLibrary module ================================= WARNING: autodoc: failed to import module 'Chem.rdSubstructLibrary' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdTautomerQuery' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdchem' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdfiltercatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdfragcatalog' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdinchi' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdmolfiles' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdmolops' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdqueries' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Chem.rdtrajectory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataManip' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DataManip.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DataManip.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.fmcs.rst WARNING: autodoc: failed to import module 'DataManip.Metric' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DataManip.Metric.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Chem.fmcs.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DataManip.Metric.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DataManip.rst WARNING: autodoc: failed to import module 'DataManip.Metric.rdMetricMatrixCalc' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DataStructs.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DataManip.Metric.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DataStructs.rst:18: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DataManip.Metric.rst WARNING: autodoc: failed to import module 'DataStructs.BitEnsemble' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.BitEnsembleDb' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.BitUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.LazySignature' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.TopNContainer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.VectCollection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DataStructs.cDataStructs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Dbase.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DataStructs.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Dbase.rst:18: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DataStructs.rst WARNING: autodoc: failed to import module 'Dbase.DbConnection' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbInfo' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbModule' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbReport' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbResultSet' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.DbUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Dbase.StorageUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'DistanceGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DistanceGeometry.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Dbase.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DistanceGeometry.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Dbase.rst WARNING: autodoc: failed to import module 'DistanceGeometry.DistGeom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ForceField.rst:5: WARNING: Block quote ends without a blank line; unexpected unindent. WARNING: autodoc: failed to import module 'ForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ForceField.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DistanceGeometry.rst WARNING: autodoc: failed to import module 'ForceField.rdForceField' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Geometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Geometry.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DistanceGeometry.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Geometry.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ForceField.rst WARNING: autodoc: failed to import module 'Geometry.rdGeometry' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.DataManip.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.rst:24: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Geometry.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.rst:38: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Geometry.rst WARNING: autodoc: failed to import module 'ML.AnalyzeComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.BuildComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Cluster.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Cluster.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.rst WARNING: autodoc: failed to import module 'ML.Cluster.Butina' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.ClusterUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.ClusterVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Clustering' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Clusters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Murtagh' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Resemblance' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Cluster.Standardize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Composite.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Cluster.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Composite.rst:14: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Cluster.rst WARNING: autodoc: failed to import module 'ML.Composite.AdjustComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite.BayesComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Composite.Composite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.CompositeRun' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Data.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Composite.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Data.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Composite.rst WARNING: autodoc: failed to import module 'ML.Data.DataUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.FindQuantBounds' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.MLData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.Quantize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.SplitData' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.Stats' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.Transforms' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Data.cQuantize' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.DecTree.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Data.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.DecTree.rst:23: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Data.rst WARNING: autodoc: failed to import module 'ML.DecTree.BuildQuantTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.BuildSigTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.DecTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.Forest' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.ID3' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.PruneTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.QuantTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.SigTree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.Tree' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.TreeUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.DecTree.TreeVis' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Descriptors.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.DecTree.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Descriptors.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.DecTree.rst WARNING: autodoc: failed to import module 'ML.Descriptors.CompoundDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.Descriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.MoleculeDescriptors' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Descriptors.Parser' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.EnrichPlot' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.GrowComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.InfoTheory.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Descriptors.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.InfoTheory.rst:15: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Descriptors.rst WARNING: autodoc: failed to import module 'ML.InfoTheory.BitClusterer' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory.BitRank' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.InfoTheory.entropy' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.InfoTheory.rdInfoTheory.rst:2: WARNING: Title underline too short. rdkit.ML.InfoTheory.rdInfoTheory module ====================================== WARNING: autodoc: failed to import module 'ML.InfoTheory.rdInfoTheory' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.KNN.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.InfoTheory.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.KNN.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.InfoTheory.rst WARNING: autodoc: failed to import module 'ML.KNN.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.DistFunctions' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.KNNClassificationModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.KNNModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.KNN.KNNRegressionModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.MLUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.MLUtils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.KNN.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.MLUtils.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.KNN.rst WARNING: autodoc: failed to import module 'ML.MLUtils.VoteImg' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.MatOps' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ModelPackage' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.ModelPackage.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.MLUtils.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.ModelPackage.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.MLUtils.rst WARNING: autodoc: failed to import module 'ML.ModelPackage.PackageUtils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ModelPackage.Packager' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.NaiveBayes' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.NaiveBayes.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.ModelPackage.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.NaiveBayes.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.ModelPackage.rst WARNING: autodoc: failed to import module 'ML.NaiveBayes.ClassificationModel' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.NaiveBayes.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Neural.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.NaiveBayes.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Neural.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.NaiveBayes.rst WARNING: autodoc: failed to import module 'ML.Neural.ActFuncs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.CrossValidate' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.NetNode' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.Network' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Neural.Trainers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.SLT' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.SLT.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Neural.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.SLT.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Neural.rst WARNING: autodoc: failed to import module 'ML.SLT.Risk' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Scoring.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.SLT.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Scoring.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.SLT.rst WARNING: autodoc: failed to import module 'ML.Scoring.Scoring' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.ScreenComposite' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'ML.files' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'Numerics' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Numerics.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Scoring.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Numerics.rst:12: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.Scoring.rst WARNING: autodoc: failed to import module 'Numerics.rdAlignment' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDConfig' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDLogger' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDPaths' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'RDRandom' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'SimDivFilters' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.SimDivFilters.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Numerics.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.SimDivFilters.rst:13: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.Numerics.rst WARNING: autodoc: failed to import module 'SimDivFilters.SimilarityPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'SimDivFilters.rdSimDivPickers' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'TestRunner' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.VLib.rst:5: WARNING: duplicate label subpackages, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.ML.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.VLib.rst:12: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.SimDivFilters.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.VLib.rst:23: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.SimDivFilters.rst WARNING: autodoc: failed to import module 'VLib.Filter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Node' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.VLib.NodeLib.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.VLib.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.VLib.NodeLib.rst:19: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.VLib.rst WARNING: autodoc: failed to import module 'VLib.NodeLib.DbMolSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.DbPickleSupplier' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SDSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsMolFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmartsRemover' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesDupeFilter' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesOutput' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.NodeLib.SmilesSupply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Output' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Supply' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'VLib.Transform' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'rdBase' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'six' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.utils.rst:5: WARNING: duplicate label submodules, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.VLib.NodeLib.rst /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.utils.rst:16: WARNING: duplicate label module contents, other instance in /build/reproducible-path/rdkit-202209.3/Docs/Book/source/rdkit.VLib.NodeLib.rst WARNING: autodoc: failed to import module 'utils.cactvs' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.chemutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.fileutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.listutils' from module 'rdkit'; the following exception was raised: No module named 'rdkit' WARNING: autodoc: failed to import module 'utils.spiral' from module 'rdkit'; the following exception was raised: No module named 'rdkit' looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/rdkit-202209.3/Docs/Book/data/README.md: WARNING: document isn't included in any toctree /build/reproducible-path/rdkit-202209.3/Docs/Book/source/modules.rst: WARNING: document isn't included in any toctree done processing RDKit.tex... index Overview Install GettingStartedInPython RDKit_Book Cartridge BackwardsIncompatibleChanges api-docs source/rdkit source/rdkit.Avalon source/rdkit.Avalon.pyAvalonTools source/rdkit.Chem source/rdkit.Chem.AtomPairs source/rdkit.Chem.AtomPairs.Pairs source/rdkit.Chem.AtomPairs.Sheridan source/rdkit.Chem.AtomPairs.Torsions source/rdkit.Chem.AtomPairs.Utils source/rdkit.Chem.ChemUtils source/rdkit.Chem.ChemUtils.AlignDepict source/rdkit.Chem.ChemUtils.BulkTester source/rdkit.Chem.ChemUtils.DescriptorUtilities source/rdkit.Chem.ChemUtils.SDFToCSV source/rdkit.Chem.ChemUtils.TemplateExpand source/rdkit.Chem.Draw source/rdkit.Chem.Draw.IPythonConsole source/rdkit.Chem.Draw.MolDrawing source/rdkit.Chem.Draw.SimilarityMaps source/rdkit.Chem.Draw.rdMolDraw2D source/rdkit.Chem.Draw.rdMolDraw2DQt source/rdkit.Chem.Draw.aggCanvas source/rdkit.Chem.Draw.cairoCanvas source/rdkit.Chem.Draw.canvasbase source/rdkit.Chem.Draw.mplCanvas source/rdkit.Chem.Draw.qtCanvas source/rdkit.Chem.EState source/rdkit.Chem.EState.AtomTypes source/rdkit.Chem.EState.EState source/rdkit.Chem.EState.EState_VSA source/rdkit.Chem.EState.Fingerprinter source/rdkit.Chem.FeatMaps source/rdkit.Chem.FeatMaps.FeatMapParser source/rdkit.Chem.FeatMaps.FeatMapPoint source/rdkit.Chem.FeatMaps.FeatMapUtils source/rdkit.Chem.FeatMaps.FeatMaps source/rdkit.Chem.Features source/rdkit.Chem.Features.FeatDirUtilsRD source/rdkit.Chem.Features.ShowFeats source/rdkit.Chem.Fingerprints source/rdkit.Chem.Fingerprints.ClusterMols source/rdkit.Chem.Fingerprints.DbFpSupplier source/rdkit.Chem.Fingerprints.FingerprintMols source/rdkit.Chem.Fingerprints.MolSimilarity source/rdkit.Chem.Fingerprints.SimilarityScreener source/rdkit.Chem.Fraggle source/rdkit.Chem.Fraggle.FraggleSim source/rdkit.Chem.MolDb source/rdkit.Chem.MolDb.FingerprintUtils source/rdkit.Chem.MolDb.Loader source/rdkit.Chem.MolDb.Loader_orig source/rdkit.Chem.MolDb.Loader_sa source/rdkit.Chem.MolKey source/rdkit.Chem.MolKey.InchiInfo source/rdkit.Chem.MolKey.MolKey source/rdkit.Chem.Pharm2D source/rdkit.Chem.Pharm2D.Generate source/rdkit.Chem.Pharm2D.Gobbi_Pharm2D source/rdkit.Chem.Pharm2D.Matcher source/rdkit.Chem.Pharm2D.SigFactory source/rdkit.Chem.Pharm2D.Utils source/rdkit.Chem.Pharm3D source/rdkit.Chem.Pharm3D.EmbedLib source/rdkit.Chem.Pharm3D.ExcludedVolume source/rdkit.Chem.Pharm3D.Pharmacophore source/rdkit.Chem.Scaffolds source/rdkit.Chem.Scaffolds.MurckoScaffold source/rdkit.Chem.Scaffolds.rdScaffoldNetwork source/rdkit.Chem.SimpleEnum source/rdkit.Chem.SimpleEnum.Enumerator source/rdkit.Chem.Subshape source/rdkit.Chem.Subshape.BuilderUtils source/rdkit.Chem.Subshape.SubshapeAligner source/rdkit.Chem.Subshape.SubshapeBuilder source/rdkit.Chem.Subshape.SubshapeObjects source/rdkit.Chem.Suppliers source/rdkit.Chem.Suppliers.DbMolSupplier source/rdkit.Chem.Suppliers.MolSupplier source/rdkit.Chem.fmcs source/rdkit.Chem.fmcs.fmcs source/rdkit.Chem.AllChem source/rdkit.Chem.BRICS source/rdkit.Chem.BuildFragmentCatalog source/rdkit.Chem.ChemicalFeatures source/rdkit.Chem.ChemicalForceFields source/rdkit.Chem.Crippen source/rdkit.Chem.Descriptors source/rdkit.Chem.Descriptors3D source/rdkit.Chem.EnumerateHeterocycles source/rdkit.Chem.EnumerateStereoisomers source/rdkit.Chem.FastSDMolSupplier source/rdkit.Chem.FeatFinderCLI source/rdkit.Chem.FilterCatalog source/rdkit.Chem.FragmentCatalog source/rdkit.Chem.FragmentMatcher source/rdkit.Chem.Fragments source/rdkit.Chem.FunctionalGroups source/rdkit.Chem.GraphDescriptors source/rdkit.Chem.Graphs source/rdkit.Chem.Lipinski source/rdkit.Chem.MACCSkeys source/rdkit.Chem.MCS source/rdkit.Chem.MolCatalog source/rdkit.Chem.MolStandardize source/rdkit.Chem.MolStandardize.rdMolStandardize source/rdkit.Chem.MolSurf source/rdkit.Chem.PandasTools source/rdkit.Chem.PeriodicTable source/rdkit.Chem.PropertyMol source/rdkit.Chem.PyMol source/rdkit.Chem.QED source/rdkit.Chem.Randomize source/rdkit.Chem.Recap source/rdkit.Chem.ReducedGraphs source/rdkit.Chem.RegistrationHash source/rdkit.Chem.SATIS source/rdkit.Chem.SaltRemover source/rdkit.Chem.ShowMols source/rdkit.Chem.TemplateAlign source/rdkit.Chem.TorsionFingerprints source/rdkit.Chem.inchi source/rdkit.Chem.rdchem source/rdkit.Chem.rdDistGeom source/rdkit.Chem.rdqueries source/rdkit.Chem.rdFMCS source/rdkit.Chem.rdMolAlign source/rdkit.Chem.rdMolHash source/rdkit.Chem.rdReducedGraphs source/rdkit.Chem.rdtrajectory source/rdkit.Chem.rdMolTransforms source/rdkit.Chem.rdmolfiles source/rdkit.Chem.rdPartialCharges source/rdkit.Chem.rdMolCatalog source/rdkit.Chem.rdCoordGen source/rdkit.Chem.rdMolChemicalFeatures source/rdkit.Chem.rdMMPA source/rdkit.Chem.rdRGroupDecomposition source/rdkit.Chem.rdForceFieldHelpers source/rdkit.Chem.rdDepictor source/rdkit.Chem.rdChemicalFeatures source/rdkit.Chem.rdmolops source/rdkit.Chem.rdFreeSASA source/rdkit.Chem.rdMolInterchange source/rdkit.Chem.rdShapeHelpers source/rdkit.Chem.rdinchi source/rdkit.Chem.rdChemReactions source/rdkit.Chem.rdSubstructLibrary source/rdkit.Chem.rdfiltercatalog source/rdkit.Chem.rdfragcatalog source/rdkit.Chem.rdMolDescriptors source/rdkit.Chem.rdFingerprintGenerator source/rdkit.Chem.rdMHFPFingerprint source/rdkit.Chem.rdSLNParse source/rdkit.Chem.rdAbbreviations source/rdkit.Chem.rdDeprotect source/rdkit.Chem.rdMolEnumerator source/rdkit.Chem.rdCIPLabeler source/rdkit.Chem.rdTautomerQuery source/rdkit.Chem.rdEHTTools source/rdkit.DataManip source/rdkit.DataManip.Metric source/rdkit.DataManip.Metric.rdMetricMatrixCalc source/rdkit.DataStructs source/rdkit.DataStructs.BitEnsemble source/rdkit.DataStructs.BitEnsembleDb source/rdkit.DataStructs.BitUtils source/rdkit.DataStructs.LazySignature source/rdkit.DataStructs.TopNContainer source/rdkit.DataStructs.VectCollection source/rdkit.DataStructs.cDataStructs source/rdkit.Dbase source/rdkit.Dbase.DbConnection source/rdkit.Dbase.DbInfo source/rdkit.Dbase.DbModule source/rdkit.Dbase.DbReport source/rdkit.Dbase.DbResultSet source/rdkit.Dbase.DbUtils source/rdkit.Dbase.StorageUtils source/rdkit.DistanceGeometry source/rdkit.DistanceGeometry.DistGeom source/rdkit.ForceField source/rdkit.ForceField.rdForceField source/rdkit.Geometry source/rdkit.Geometry.rdGeometry source/rdkit.ML source/rdkit.ML.Cluster source/rdkit.ML.Cluster.Butina source/rdkit.ML.Cluster.ClusterUtils source/rdkit.ML.Cluster.ClusterVis source/rdkit.ML.Cluster.Clusters source/rdkit.ML.Cluster.Murtagh source/rdkit.ML.Cluster.Resemblance source/rdkit.ML.Cluster.Standardize source/rdkit.ML.Cluster.Clustering source/rdkit.ML.Composite source/rdkit.ML.Composite.AdjustComposite source/rdkit.ML.Composite.BayesComposite source/rdkit.ML.Composite.Composite source/rdkit.ML.Data source/rdkit.ML.Data.DataUtils source/rdkit.ML.Data.FindQuantBounds source/rdkit.ML.Data.MLData source/rdkit.ML.Data.Quantize source/rdkit.ML.Data.cQuantize source/rdkit.ML.Data.SplitData source/rdkit.ML.Data.Stats source/rdkit.ML.Data.Transforms source/rdkit.ML.DecTree source/rdkit.ML.DecTree.BuildQuantTree source/rdkit.ML.DecTree.BuildSigTree source/rdkit.ML.DecTree.CrossValidate source/rdkit.ML.DecTree.DecTree source/rdkit.ML.DecTree.Forest source/rdkit.ML.DecTree.ID3 source/rdkit.ML.DecTree.PruneTree source/rdkit.ML.DecTree.QuantTree source/rdkit.ML.DecTree.SigTree source/rdkit.ML.DecTree.Tree source/rdkit.ML.DecTree.TreeUtils source/rdkit.ML.DecTree.TreeVis source/rdkit.ML.Descriptors source/rdkit.ML.Descriptors.CompoundDescriptors source/rdkit.ML.Descriptors.Descriptors source/rdkit.ML.Descriptors.MoleculeDescriptors source/rdkit.ML.Descriptors.Parser source/rdkit.ML.InfoTheory source/rdkit.ML.InfoTheory.BitClusterer source/rdkit.ML.InfoTheory.BitRank source/rdkit.ML.InfoTheory.entropy source/rdkit.ML.InfoTheory.rdInfoTheory source/rdkit.ML.KNN source/rdkit.ML.KNN.CrossValidate source/rdkit.ML.KNN.DistFunctions source/rdkit.ML.KNN.KNNClassificationModel source/rdkit.ML.KNN.KNNModel source/rdkit.ML.KNN.KNNRegressionModel source/rdkit.ML.MLUtils source/rdkit.ML.MLUtils.VoteImg source/rdkit.ML.ModelPackage source/rdkit.ML.ModelPackage.PackageUtils source/rdkit.ML.ModelPackage.Packager source/rdkit.ML.NaiveBayes source/rdkit.ML.NaiveBayes.ClassificationModel source/rdkit.ML.NaiveBayes.CrossValidate source/rdkit.ML.Neural source/rdkit.ML.Neural.ActFuncs source/rdkit.ML.Neural.CrossValidate source/rdkit.ML.Neural.NetNode source/rdkit.ML.Neural.Network source/rdkit.ML.Neural.Trainers source/rdkit.ML.SLT source/rdkit.ML.SLT.Risk source/rdkit.ML.Scoring source/rdkit.ML.Scoring.Scoring source/rdkit.ML.AnalyzeComposite source/rdkit.ML.BuildComposite source/rdkit.ML.CompositeRun source/rdkit.ML.EnrichPlot source/rdkit.ML.GrowComposite source/rdkit.ML.MatOps source/rdkit.ML.ScreenComposite source/rdkit.ML.files source/rdkit.Numerics source/rdkit.Numerics.rdAlignment source/rdkit.SimDivFilters source/rdkit.SimDivFilters.SimilarityPickers source/rdkit.SimDivFilters.rdSimDivPickers source/rdkit.VLib source/rdkit.VLib.NodeLib source/rdkit.VLib.NodeLib.DbMolSupply source/rdkit.VLib.NodeLib.DbPickleSupplier source/rdkit.VLib.NodeLib.SDSupply source/rdkit.VLib.NodeLib.SmartsMolFilter source/rdkit.VLib.NodeLib.SmartsRemover source/rdkit.VLib.NodeLib.SmilesDupeFilter source/rdkit.VLib.NodeLib.SmilesOutput source/rdkit.VLib.NodeLib.SmilesSupply source/rdkit.VLib.Filter source/rdkit.VLib.Node source/rdkit.VLib.Output source/rdkit.VLib.Supply source/rdkit.VLib.Transform source/rdkit.utils source/rdkit.utils.cactvs source/rdkit.utils.chemutils source/rdkit.utils.fileutils source/rdkit.utils.listutils source/rdkit.utils.spiral source/rdkit.rdBase source/rdkit.RDConfig source/rdkit.RDLogger source/rdkit.RDPaths source/rdkit.RDRandom source/rdkit.TestRunner source/rdkit.six GettingStartedInC++ resolving references... /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInC++.md:147: WARNING: None:any reference target not found: ./C++Examples/example1.cpp /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInC++.md:169: WARNING: None:any reference target not found: ./C++Examples/example1.cpp /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInC++.md:183: WARNING: None:any reference target not found: ./C++Examples/example1.cpp /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInC++.md:196: WARNING: None:any reference target not found: 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[1] [2] Chapter 1. (/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) Underfull \hbox (badness 10000) in paragraph at lines 125--127 []\T1/qtm/m/n/10 Chem-in-for-mat-ics nodes for KN-IME (dis-tributed from the KN -IME com-mu-nity site: [1] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) LaTeX Warning: Hyper reference `Overview:footnote1' on page 2 undefined on inpu t line 275. [2] [3] [4] Chapter 2. 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[17] [18] [19] [20] LaTeX Warning: Hyper reference `GettingStartedInPython:chem-vs-allchem' on page 21 undefined on input line 1587. [21] [22] [23] [24] LaTeX Warning: Hyper reference `GettingStartedInPython:the-sssr-problem' on pag e 25 undefined on input line 1828. [25] [26] Underfull \hbox (badness 10000) in paragraph at lines 1978--1981 []\T1/qtm/m/n/10 An-other op-tion for Com-pute2DCoords al-lows you to gen-er-at e 2D de-pic-tions for molecules that Underfull \hbox (badness 10000) in paragraph at lines 1978--1981 \T1/qtm/m/n/10 closely mimic 3D con-form-ers. This is avail-able us-ing the fun c-tion \T1/txtt/m/n/10 rdkit.Chem.AllChem. Underfull \hbox (badness 10000) in paragraph at lines 2003--2009 []\T1/qtm/m/n/10 More fine-grained con-trol can be ob-tained us-ing the core fu nc-tion \T1/txtt/m/n/10 rdkit.Chem.rdDepictor. 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[107 <./picture_10.jpg>] [108] [109 <./ary_group.png>] [110] Underfull \hbox (badness 10000) in paragraph at lines 10183--10183 []\T1/qtm/m/n/10 _Chi-ral-i-ty-Pos-si- Underfull \hbox (badness 10000) in paragraph at lines 10183--10183 []\T1/qtm/m/n/10 _Re-ac-tion-De- Underfull \hbox (badness 10000) in paragraph at lines 10183--10183 []\T1/qtm/m/n/10 mo-lAtomMap- Underfull \hbox (badness 10000) in paragraph at lines 10183--10183 []\T1/qtm/m/n/10 molFileIn-ver- Underfull \hbox (badness 10000) in paragraph at lines 10183--10183 []\T1/qtm/m/n/10 mol-Rxn-Com-po- [111] [112] [113] Underfull \hbox (badness 10000) in paragraph at lines 10345--10350 []\T1/qtm/m/n/10 By de-fault the \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles.SDMolSup plier \T1/qtm/m/n/10 and \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles. Underfull \hbox (badness 10000) in paragraph at lines 10394--10397 []\T1/qtm/m/n/10 This be-hav-ior is en-abled by de-fault and can be turned on/o ff with the \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles. Underfull \hbox (badness 10000) in paragraph at lines 10398--10402 \T1/qtm/m/n/10 tions \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles.CreateAtomStringProp ertyList()\T1/qtm/m/n/10 , \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles. [114] Underfull \hbox (badness 10000) in paragraph at lines 10542--10542 []\T1/qhv/m/n/10 Mix- Underfull \hbox (badness 10000) in paragraph at lines 10542--10542 []\T1/qtm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 10542--10542 []\T1/qtm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 10542--10542 []\T1/qtm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 10542--10542 []\T1/qtm/m/n/10 mix- [115] [116 <./enhanced_stereo_and1_and2_base.png> <./enhanced_stereo_and1_and2_ expand.png> <./enhanced_stereo_and1_cis_base.png> <./enhanced_stereo_and1_cis_e xpand.png> <./enhanced_stereo_and1_trans_base.png> <./enhanced_stereo_and1_tran s_expand.png> <./enhanced_stereo_or1_or2_base.png> <./enhanced_stereo_or1_cis_b ase.png> <./enhanced_stereo_or1_trans_base.png> <./enhanced_stereo_abs_and_base .png> <./enhanced_stereo_abs_and_expand.png> <./enhanced_stereo_abs_or_base.png >] Underfull \hbox (badness 10000) in paragraph at lines 10559--10562 []\T1/qtm/m/n/10 It is pos-si-ble to enu-mer-ate the el-e-ments of a \T1/txtt/m /n/10 StereoGroup \T1/qtm/m/n/10 us-ing the func-tion \T1/txtt/m/n/10 rdkit.Che m. [117] [118 <./EnhancedStereoSSS_molA.png> <./EnhancedStereoSSS_molB.png> <./Enh ancedStereoSSS_molC.png> <./EnhancedStereoSSS_molD.png> <./EnhancedStereoSSS_mo lE.png> <./EnhancedStereoSSS_molF.png> <./EnhancedStereoSSS_molG.png>] [119 <./ query_bonds.png>] [120 <./query_bonds.2.png> <./query_atoms.png>] [121] [122] [123] Underfull \hbox (badness 10000) in paragraph at lines 11247--11257 []\T1/txtt/m/n/10 allowNontetrahedralChirality\T1/qtm/m/n/10 : when this is \T1 /txtt/m/n/10 true \T1/qtm/m/n/10 non-tetrahedral chi-ral-ity will be per- Underfull \hbox (badness 10000) in paragraph at lines 11247--11257 \T1/qtm/m/n/10 ceived from 3D co-or-di-nates. The de-fault value is \T1/txtt/m/ n/10 true \T1/qtm/m/n/10 un-less the en-vi-ron-ment vari- Underfull \hbox (badness 10000) in paragraph at lines 11247--11257 \T1/qtm/m/n/10 able \T1/txtt/m/n/10 RDK_ENABLE_NONTETRAHEDRAL_STEREO \T1/qtm/m/ n/10 is set to \T1/txtt/m/n/10 "0"\T1/qtm/m/n/10 . Can set/checked from Underfull \hbox (badness 10000) in paragraph at lines 11247--11257 \T1/qtm/m/n/10 C++ us-ing the func-tions \T1/txtt/m/n/10 RDKit::Chirality::setA llowNontetrahedralChirality() \T1/qtm/m/n/10 / Underfull \hbox (badness 10000) in paragraph at lines 11247--11257 \T1/txtt/m/n/10 RDKit::Chirality::getAllowNontetrahedralChirality() \T1/qtm/m/n /10 or from Python us-ing the func-tions Underfull \hbox (badness 10000) in paragraph at lines 11259--11269 []\T1/txtt/m/n/10 useLegacyStereoPerception\T1/qtm/m/n/10 : when this is \T1/tx tt/m/n/10 true \T1/qtm/m/n/10 the legacy im-ple-men-ta-tion for per- Underfull \hbox (badness 10000) in paragraph at lines 11259--11269 \T1/qtm/m/n/10 ceiv-ing stere-o-chem-istry will be used. The de-fault value is \T1/txtt/m/n/10 true \T1/qtm/m/n/10 un-less the en-vi-ron- Underfull \hbox (badness 10000) in paragraph at lines 11259--11269 \T1/qtm/m/n/10 ment vari-able \T1/txtt/m/n/10 RDK_USE_LEGACY_STEREO_PERCEPTION \T1/qtm/m/n/10 is set to \T1/txtt/m/n/10 "0"\T1/qtm/m/n/10 . Can set/checked Underfull \hbox (badness 10000) in paragraph at lines 11259--11269 \T1/qtm/m/n/10 from C++ us-ing the func-tions \T1/txtt/m/n/10 RDKit::Chirality: :setUseLegacyStereoPerception() \T1/qtm/m/n/10 / [124] Chapter 5. [125] [126] [127] [128] [129] Overfull \hbox (1052.74055pt too wide) in paragraph at lines 11571--11571 []\T1/txtt/m/n/10 CC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)[C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\ T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/1 0 ][]2[]CCCN2C([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ]([C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)CC)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/t xtt/m/n/10 ](CO)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)NC([]=[] O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ]([C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/ m/n/10 ](C)O)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CSSC [C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](NC1[]=[]O)C([]=[]O)N[C[]@[][]\T1/txt t/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1cnc[nH][]1[])C([]=[]O)N[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txt t/m/n/10 ](CCCNC([]=[]N)N)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/ 10 ](Cc1c[nH]c3ccccc13)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCCNC([]=[]N)N)C([]=[]O)N2| Overfull \hbox (149.74318pt too wide) in paragraph at lines 11573--11573 []\T1/txtt/m/n/10 CN1C([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCCNC( []=[]N)N)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccc(O)cc2 )NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O)[C []\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccc3ccccc3c2)NC([]=[]O)[C[]@[][]\T1 /txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]CC([]=[]O)O| Overfull \hbox (97.24333pt too wide) in paragraph at lines 11574--11574 []\T1/txtt/m/n/10 NCCCC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](NC([]=[]O)[C[ ]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1ccc(OP([]=[]O)(O)O)cc1)NC([]=[]O)Cc1 ccccc1)C([]=[]O)N1CCC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]C([]=[]O)N[ C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1ccccc1)C(N)[]=[]O| Overfull \hbox (643.24174pt too wide) in paragraph at lines 11575--11575 []\T1/txtt/m/n/10 CCCCCCCCCCCCCCCCNC([]=[]O)CN(CC([]=[]O)NC(C)(C)C([]=[]O)N[C[] @[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/tx tt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC(C)C)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[ ]\T1/txtt/m/n/10 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m /n/10 ](CCCNC([]=[]N)N)C([]=[]O)N1CCC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ] []1[]C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCCNC([]=[]N)N)C ([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC(N)[]=[]O)C(N)[]=[]O )C([]=[]O)c1cccnc1| Overfull \hbox (464.74226pt too wide) in paragraph at lines 11576--11576 []\T1/txtt/m/n/10 CCCCCCCCCCCCCCCCN(CCCCCCCCCCCCCCCC)CCCCCC([]=[]O)NC(C)(C)C([] =[]O)NC(Cc1ccccc1)C([]=[]O)NC(CC(C)C)C([]=[]O)NC(Cc1ccccc1)C([]=[]O)NC(CCCNC([] =[]N)N)C([]=[]O)N1CCCC1C([]=[]O)NC(CCCNC([]=[]N)N)C([]=[]O)NC(CC(N)[]=[]O)C(N)[ ]=[]O| Overfull \hbox (359.74257pt too wide) in paragraph at lines 11577--11577 []\T1/txtt/m/n/10 CC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)[C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/tx tt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC(C )C)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O) [C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt/bx/ n/10 @H[]\T1/txtt/m/n/10 ](C(C)C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/ n/10 ](CC(C)C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCSC)NC1[]=[ ]O| Overfull \hbox (370.24254pt too wide) in paragraph at lines 11578--11578 []\T1/txtt/m/n/10 CC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)[C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/tx tt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC(C )C)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O) [C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt/bx/ n/10 @H[]\T1/txtt/m/n/10 ](C(C)C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/ n/10 ](CC(C)C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC[S[]+[]](C )[O[]- Overfull \hbox (422.74239pt too wide) in paragraph at lines 11579--11579 []\T1/txtt/m/n/10 CC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)[C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/tx tt/m/n/10 ](Cc2c[nH]c3ccccc23)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/1 0 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccccc2)NC ([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O)[C[]\ T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCSC)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\ T1/txtt/m/n/10 ](CC(C)C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC [S[]+[]](C)[O[]- Overfull \hbox (249.49289pt too wide) in paragraph at lines 11580--11580 [][]\T1/txtt/m/n/10 ])NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C(C) C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2c[nH]c3ccccc23)NC([]= []O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt /bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H []\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC[S[]+[]](C)[O[]- Overfull \hbox (1052.74055pt too wide) in paragraph at lines 11594--11594 []\T1/txtt/m/n/10 CC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)[C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\ T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/1 0 ][]2[]CCCN2C([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ]([C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)CC)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/t xtt/m/n/10 ](CO)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)NC([]=[] O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ]([C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/ m/n/10 ](C)O)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CSSC [C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](NC1[]=[]O)C([]=[]O)N[C[]@[][]\T1/txt t/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1cnc[nH][]1[])C([]=[]O)N[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txt t/m/n/10 ](CCCNC([]=[]N)N)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/ 10 ](Cc1c[nH]c3ccccc13)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCCNC([]=[]N)N)C([]=[]O)N2| Overfull \hbox (149.74318pt too wide) in paragraph at lines 11596--11596 []\T1/txtt/m/n/10 CN1C([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCCNC( []=[]N)N)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccc(O)cc2 )NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O)[C []\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccc3ccccc3c2)NC([]=[]O)[C[]@[][]\T1 /txtt/bx/n/10 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[169] [170] [171] Underfull \hbox (badness 10000) in paragraph at lines 14914--14918 \T1/qtm/m/n/10 Groups of molecules are read us-ing a Sup-plier (for ex-am-ple, an \T1/txtt/m/n/10 RDKit::SDMolSupplier \T1/qtm/m/n/10 or an [172] [173] [174] [175] [176] [177] [178] Underfull \hbox (badness 6691) in paragraph at lines 15454--15456 []\T1/qtm/m/n/10 The \T1/txtt/m/n/10 auto\TS1/txtt/m/n/10 ' \T1/txtt/m/n/10 key word here is hiding the fact that \T1/qtm/m/n/10 get-Bond-Be-tweenAtoms\T1/txtt /m/n/10 returns the index of the [179] [180] LaTeX Warning: Hyper reference `GettingStartedInC++:TheSSSRProblem' on page 181 undefined on input line 15582. LaTeX Warning: Hyper reference `GettingStartedInC++:twoAddHs' on page 181 undef ined on input line 15612. [181] [182] Overfull \vbox (1.27959pt too high) detected at line 15784 [183] LaTeX Warning: Hyper reference `GettingStartedInC++:blaney' on page 184 undefin ed on input line 15802. LaTeX Warning: Hyper reference `GettingStartedInC++:rappe' on page 184 undefine d on input line 15837. LaTeX Warning: Hyper reference `GettingStartedInC++:riniker2' on page 184 undef ined on input line 15841. [184] LaTeX Warning: Hyper reference `GettingStartedInC++:mmff1' on page 185 undefine d on input line 15885. LaTeX Warning: Hyper reference `GettingStartedInC++:mmff2' on page 185 undefine d on input line 15885. LaTeX Warning: Hyper reference `GettingStartedInC++:mmff3' on page 185 undefine d on input line 15885. LaTeX Warning: Hyper reference `GettingStartedInC++:mmff4' on page 185 undefine d on input line 15886. LaTeX Warning: Hyper reference `GettingStartedInC++:mmffs' on page 185 undefine d on input line 15886. [185] [186] [187] [188] [189] Overfull \vbox (0.52191pt too high) detected at line 16321 [190] [191] LaTeX Warning: Hyper reference `GettingStartedInC++:guba' on page 192 undefined on input line 16440. [192] [193] [194] Chapter 9. [195] [196] Chapter 10. No file RDKit.ind. Package longtable Warning: Table widths have changed. Rerun LaTeX. [197] (./RDKit.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `RDKit.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ec.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r .enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc} Output written on RDKit.pdf (201 pages, 1797608 bytes). Transcript written on RDKit.log. Latexmk: Missing input file 'RDKit.toc' (or dependence on it) from following: No file RDKit.toc. Latexmk: Missing input file 'RDKit.ind' (or dependence on it) from following: No file RDKit.ind. 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(/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) Underfull \hbox (badness 10000) in paragraph at lines 125--127 []\T1/qtm/m/n/10 Chem-in-for-mat-ics nodes for KN-IME (dis-tributed from the KN -IME com-mu-nity site: [1] LaTeX Warning: Hyper reference `Overview:footnote1' on page 2 undefined on inpu t line 275. [2] [3] [4] Chapter 2. [5] [6] (/usr/share/texlive/texmf-dist/tex/latex/txfonts/ts1txtt.fd) [7] [8] Underfull \hbox (badness 10000) in paragraph at lines 764--766 []\T1/qtm/m/n/10 If you want to use the python wrap-pers: \T1/txtt/m/n/10 ./boo tstrap.sh [][]with[]libraries=python, [9] [10] Underfull \hbox (badness 10000) in paragraph at lines 931--933 []\T1/qtm/m/n/10 You can en-able sup-port for gen-er-at-ing InChI strings and I nChI keys by adding the ar-gu-ment [11] [12] [13] Underfull \hbox (badness 5490) in paragraph at lines 1182--1184 \T1/qtm/m/n/10 This sec-tion as-sumes that python is in-stalled in \T1/txtt/m/n /10 C:[]Python36 that the boost libraries have been [14] Underfull \hbox (badness 10000) in paragraph at lines 1233--1235 []\T1/txtt/m/n/10 DBOOST_ROOT=C:/boost []DRDK_BUILD_INCHI_SUPPORT=ON []DRDK_BUI LD_AVALON_SUPPORT=ON Underfull \hbox (badness 10000) in paragraph at lines 1233--1235 []\T1/txtt/m/n/10 DRDK_BUILD_PGSQL=ON []DPostgreSQL_ROOT="C:[]Program Files[]Po stgreSQL[]9.5" []G"Visual Underfull \hbox (badness 10000) in paragraph at lines 1245--1247 []\T1/txtt/m/n/10 "C:[]Program Files[]PostgreSQL[]9.5[]bin[]pg_ctl.exe" []N "po stgresql[]9.5" []D "C:[] Underfull \hbox (badness 10000) in paragraph at lines 1253--1255 []\T1/txtt/m/n/10 "C:[]Program Files[]PostgreSQL[]9.5[]bin[]pg_ctl.exe" []N "po stgresql[]9.5" []D "C:[] [15] [16] Chapter 3. [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] Underfull \hbox (badness 10000) in paragraph at lines 1978--1981 []\T1/qtm/m/n/10 An-other op-tion for Com-pute2DCoords al-lows you to gen-er-at e 2D de-pic-tions for molecules that Underfull \hbox (badness 10000) in paragraph at lines 1978--1981 \T1/qtm/m/n/10 closely mimic 3D con-form-ers. This is avail-able us-ing the fun c-tion \T1/txtt/m/n/10 rdkit.Chem.AllChem. Underfull \hbox (badness 10000) in paragraph at lines 2003--2009 []\T1/qtm/m/n/10 More fine-grained con-trol can be ob-tained us-ing the core fu nc-tion \T1/txtt/m/n/10 rdkit.Chem.rdDepictor. [27 <./picture_1.png (PNG copy)> <./picture_0.png (PNG copy)> <./picture_3.png (PNG copy)> <./picture_2.png> <./picture_4.png>] [28] [29] [30] [31 <./cdk2_mol 1.png> <./cdk2_mol2.png> <./cdk2_molgrid.png (PNG copy)>] [32 <./cdk2_molgrid_a ligned.png (PNG copy)>] [33 <./atom_highlights_1.png>] [34 <./atom_highlights_2 .png> <./atom_highlights_3.png>] Overfull \vbox (2.78867pt too high) detected at line 2452 [35 <./atom_annotation_1.png> <./atom_labels_1.png>] [36 <./atom_labels_2.png>] [37 <./atom_labels_3.png> <./mol_metadata1.png>] [38] [39] [40] [41 <./substruc t_search_parameters1.png>] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51 <./mfp2_bit872.png> <./rdk_bit1553.png> <./rdk_bit1553_2.png>] [52] [53 <./similarity_map_fp1.png>] [54 <./similarity_map_fp2.png>] Overfull \vbox (2.07828pt too high) detected at line 3667 [55 <./similarity_map_fp3.png>] [56] [57 <./similarity_map_charges.png>] [58 <./similarity_map_crippen.png>] [59] Overfull \hbox (44.74348pt too wide) in paragraph at lines 3825--3825 []\T1/txtt/m/n/10 [cH:5]1[cH:6][c:7]2[cH:8][n:9][cH:10][cH:11][c:12]2[c:3]([cH: 4]1)[C:2](=[O:1])[N:13]=[N+:14]=[N- [60 <./reaction1.png>] [61 <./reaction1_highlight.png>] [62] [63] [64] Overfull \vbox (1.6561pt too high) detected at line 4212 [65] [66] [67] [68] [69] Overfull \vbox (1.11137pt too high) detected at line 4550 [70] [71] [72] [73 <./picture_6.png>] [74] Overfull \hbox (520.84497pt too wide) in alignment at lines 4824--4826 [] [] [] Overfull \hbox (520.84497pt too wide) in alignment at lines 4826--4832 [] [] [] Overfull \hbox (520.84497pt too wide) in alignment at lines 4832--4838 [] [] [] Overfull \hbox (520.84497pt too wide) in alignment at lines 4838--4840 [] [] [] Overfull \hbox (520.84497pt too wide) in alignment at lines 4840--5271 [] [] [] [75] Underfull \hbox (badness 10000) in paragraph at lines 5463--5463 []\T1/qtm/m/n/10 De-scrip- Overfull \hbox (19.56651pt too wide) in paragraph at lines 5463--5463 \T1/qtm/m/n/10 tor/Descriptor Overfull 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in paragraph at lines 5649--5649 []\T1/qtm/m/n/10 Ba- Underfull \hbox (badness 10000) in paragraph at lines 5649--5649 []\T1/txtt/m/n/10 [#7;+,$([N;H2&+0][$([C,a]);!$([C,a](=O))]),$([N;H1&+0]([$([C, a]);!$([C, Underfull \hbox (badness 10000) in paragraph at lines 5649--5649 \T1/txtt/m/n/10 a](=O))])[$([C,a]);!$([C,a](=O))]),$([N;H0&+0]([C;!$(C(=O))])([ C;!$(C(=O))])[C;! Overfull \hbox (7.26567pt too wide) in paragraph at lines 5649--5649 []\T1/qtm/m/n/10 Acidic| [78 <./picture_5.png (PNG copy)>] [79] [80] Chapter 4. [81 <./picture_9.png (PNG copy)>] [82 <./picture_8.png> <./picture_7.png (PNG c opy)>] [83 <./picture_10.png> <./picture_12.png>] [84 <./picture_11.png>] [85] [86] [87] [88] [89] [90] [91] [92 <./parastereo_2.png> <./parastereo_1.png >] [93 <./potential_stereo_double_bond1.png> <./potential_stereo_double_bond2.p ng> <./potential_stereo_double_bond3.png>] [94] [95] [96 <./nontetstereo_sp1.pn g> <./nontetstereo_sp2.png> <./nontetstereo_sp3.png> <./nontetstereo_sp4.png> < ./nontetstereo_tb2.png>] [97 <./nontetstereo_tb1.png> <./nontetstereo_oh2.png>] [98 <./nontetstereo_oh1.png>] Underfull \hbox (badness 10000) in paragraph at lines 8891--8893 []\T1/qtm/m/n/10 The clas-sic ex-am-ple of this is cis-platin - \T1/txtt/m/n/10 Cl[Pt@SP1](Cl)(<[][NH3])<[][NH3] \T1/qtm/m/n/10 - vs trans-platin - [99 <./nontetstereo_ex1.png> <./nontetstereo_ex2.png> <./nontetstereo_missing1. png>] [100] [101] [102] [103] [104] [105] [106] [107 <./picture_10.jpg>] [108] [109 <./ary_group.png>] [110] Underfull \hbox (badness 10000) in paragraph at lines 10183--10183 []\T1/qtm/m/n/10 _Chi-ral-i-ty-Pos-si- Underfull \hbox (badness 10000) in paragraph at lines 10183--10183 []\T1/qtm/m/n/10 _Re-ac-tion-De- Underfull \hbox (badness 10000) in paragraph at lines 10183--10183 []\T1/qtm/m/n/10 mo-lAtomMap- Underfull \hbox (badness 10000) in paragraph at lines 10183--10183 []\T1/qtm/m/n/10 molFileIn-ver- Underfull \hbox (badness 10000) in paragraph at lines 10183--10183 []\T1/qtm/m/n/10 mol-Rxn-Com-po- [111] [112] [113] Underfull \hbox (badness 10000) in paragraph at lines 10345--10350 []\T1/qtm/m/n/10 By de-fault the \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles.SDMolSup plier \T1/qtm/m/n/10 and \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles. Underfull \hbox (badness 10000) in paragraph at lines 10394--10397 []\T1/qtm/m/n/10 This be-hav-ior is en-abled by de-fault and can be turned on/o ff with the \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles. Underfull \hbox (badness 10000) in paragraph at lines 10398--10402 \T1/qtm/m/n/10 tions \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles.CreateAtomStringProp ertyList()\T1/qtm/m/n/10 , \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles. [114] Underfull \hbox (badness 10000) in paragraph at lines 10542--10542 []\T1/qhv/m/n/10 Mix- Underfull \hbox (badness 10000) in paragraph at lines 10542--10542 []\T1/qtm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 10542--10542 []\T1/qtm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 10542--10542 []\T1/qtm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 10542--10542 []\T1/qtm/m/n/10 mix- [115] [116 <./enhanced_stereo_and1_and2_base.png> <./enhanced_stereo_and1_and2_ expand.png> <./enhanced_stereo_and1_cis_base.png> <./enhanced_stereo_and1_cis_e xpand.png> <./enhanced_stereo_and1_trans_base.png> <./enhanced_stereo_and1_tran s_expand.png> <./enhanced_stereo_or1_or2_base.png> <./enhanced_stereo_or1_cis_b ase.png> <./enhanced_stereo_or1_trans_base.png> <./enhanced_stereo_abs_and_base .png> <./enhanced_stereo_abs_and_expand.png> <./enhanced_stereo_abs_or_base.png >] Underfull \hbox (badness 10000) in paragraph at lines 10559--10562 []\T1/qtm/m/n/10 It is pos-si-ble to enu-mer-ate the el-e-ments of a \T1/txtt/m /n/10 StereoGroup \T1/qtm/m/n/10 us-ing the func-tion \T1/txtt/m/n/10 rdkit.Che m. [117] [118 <./EnhancedStereoSSS_molA.png> <./EnhancedStereoSSS_molB.png> <./Enh ancedStereoSSS_molC.png> <./EnhancedStereoSSS_molD.png> <./EnhancedStereoSSS_mo lE.png> <./EnhancedStereoSSS_molF.png> <./EnhancedStereoSSS_molG.png>] [119 <./ query_bonds.png>] [120 <./query_bonds.2.png> <./query_atoms.png>] [121] [122] [123] Underfull \hbox (badness 10000) in paragraph at lines 11247--11257 []\T1/txtt/m/n/10 allowNontetrahedralChirality\T1/qtm/m/n/10 : when this is \T1 /txtt/m/n/10 true \T1/qtm/m/n/10 non-tetrahedral chi-ral-ity will be per- Underfull \hbox (badness 10000) in paragraph at lines 11247--11257 \T1/qtm/m/n/10 ceived from 3D co-or-di-nates. The de-fault value is \T1/txtt/m/ n/10 true \T1/qtm/m/n/10 un-less the en-vi-ron-ment vari- Underfull \hbox (badness 10000) in paragraph at lines 11247--11257 \T1/qtm/m/n/10 able \T1/txtt/m/n/10 RDK_ENABLE_NONTETRAHEDRAL_STEREO \T1/qtm/m/ n/10 is set to \T1/txtt/m/n/10 "0"\T1/qtm/m/n/10 . Can set/checked from Underfull \hbox (badness 10000) in paragraph at lines 11247--11257 \T1/qtm/m/n/10 C++ us-ing the func-tions \T1/txtt/m/n/10 RDKit::Chirality::setA llowNontetrahedralChirality() \T1/qtm/m/n/10 / Underfull \hbox (badness 10000) in paragraph at lines 11247--11257 \T1/txtt/m/n/10 RDKit::Chirality::getAllowNontetrahedralChirality() \T1/qtm/m/n /10 or from Python us-ing the func-tions Underfull \hbox (badness 10000) in paragraph at lines 11259--11269 []\T1/txtt/m/n/10 useLegacyStereoPerception\T1/qtm/m/n/10 : when this is \T1/tx tt/m/n/10 true \T1/qtm/m/n/10 the legacy im-ple-men-ta-tion for per- Underfull \hbox (badness 10000) in paragraph at lines 11259--11269 \T1/qtm/m/n/10 ceiv-ing stere-o-chem-istry will be used. The de-fault value is \T1/txtt/m/n/10 true \T1/qtm/m/n/10 un-less the en-vi-ron- Underfull \hbox (badness 10000) in paragraph at lines 11259--11269 \T1/qtm/m/n/10 ment vari-able \T1/txtt/m/n/10 RDK_USE_LEGACY_STEREO_PERCEPTION \T1/qtm/m/n/10 is set to \T1/txtt/m/n/10 "0"\T1/qtm/m/n/10 . Can set/checked Underfull \hbox (badness 10000) in paragraph at lines 11259--11269 \T1/qtm/m/n/10 from C++ us-ing the func-tions \T1/txtt/m/n/10 RDKit::Chirality: :setUseLegacyStereoPerception() \T1/qtm/m/n/10 / [124] Chapter 5. [125] [126] [127] [128] [129] Overfull \hbox (1052.74055pt too wide) in paragraph at lines 11571--11571 []\T1/txtt/m/n/10 CC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)[C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\ T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/1 0 ][]2[]CCCN2C([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ]([C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)CC)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/t xtt/m/n/10 ](CO)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)NC([]=[] O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ]([C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/ m/n/10 ](C)O)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CSSC [C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](NC1[]=[]O)C([]=[]O)N[C[]@[][]\T1/txt t/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1cnc[nH][]1[])C([]=[]O)N[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txt t/m/n/10 ](CCCNC([]=[]N)N)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/ 10 ](Cc1c[nH]c3ccccc13)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCCNC([]=[]N)N)C([]=[]O)N2| Overfull \hbox (149.74318pt too wide) in paragraph at lines 11573--11573 []\T1/txtt/m/n/10 CN1C([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCCNC( []=[]N)N)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccc(O)cc2 )NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O)[C []\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccc3ccccc3c2)NC([]=[]O)[C[]@[][]\T1 /txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]CC([]=[]O)O| Overfull \hbox (97.24333pt too wide) in paragraph at lines 11574--11574 []\T1/txtt/m/n/10 NCCCC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](NC([]=[]O)[C[ ]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1ccc(OP([]=[]O)(O)O)cc1)NC([]=[]O)Cc1 ccccc1)C([]=[]O)N1CCC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]C([]=[]O)N[ C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1ccccc1)C(N)[]=[]O| Overfull \hbox (643.24174pt too wide) in paragraph at lines 11575--11575 []\T1/txtt/m/n/10 CCCCCCCCCCCCCCCCNC([]=[]O)CN(CC([]=[]O)NC(C)(C)C([]=[]O)N[C[] @[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/tx tt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC(C)C)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[ ]\T1/txtt/m/n/10 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m /n/10 ](CCCNC([]=[]N)N)C([]=[]O)N1CCC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ] []1[]C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCCNC([]=[]N)N)C ([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC(N)[]=[]O)C(N)[]=[]O )C([]=[]O)c1cccnc1| Overfull \hbox (464.74226pt too wide) in paragraph at lines 11576--11576 []\T1/txtt/m/n/10 CCCCCCCCCCCCCCCCN(CCCCCCCCCCCCCCCC)CCCCCC([]=[]O)NC(C)(C)C([] =[]O)NC(Cc1ccccc1)C([]=[]O)NC(CC(C)C)C([]=[]O)NC(Cc1ccccc1)C([]=[]O)NC(CCCNC([] =[]N)N)C([]=[]O)N1CCCC1C([]=[]O)NC(CCCNC([]=[]N)N)C([]=[]O)NC(CC(N)[]=[]O)C(N)[ ]=[]O| 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@H[]\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O) [C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt/bx/ n/10 @H[]\T1/txtt/m/n/10 ](C(C)C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/ n/10 ](CC(C)C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC[S[]+[]](C )[O[]- Overfull \hbox (422.74239pt too wide) in paragraph at lines 11579--11579 []\T1/txtt/m/n/10 CC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)[C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/tx tt/m/n/10 ](Cc2c[nH]c3ccccc23)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/1 0 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccccc2)NC ([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O)[C[]\ T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCSC)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\ T1/txtt/m/n/10 ](CC(C)C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC [S[]+[]](C)[O[]- Overfull \hbox (249.49289pt too wide) in paragraph at lines 11580--11580 [][]\T1/txtt/m/n/10 ])NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C(C) C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2c[nH]c3ccccc23)NC([]= []O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt /bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H []\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC[S[]+[]](C)[O[]- Overfull \hbox (1052.74055pt too wide) in paragraph at lines 11594--11594 []\T1/txtt/m/n/10 CC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)[C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\ T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/1 0 ][]2[]CCCN2C([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ]([C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)CC)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/t xtt/m/n/10 ](CO)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)NC([]=[] O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ]([C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/ m/n/10 ](C)O)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CSSC [C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](NC1[]=[]O)C([]=[]O)N[C[]@[][]\T1/txt t/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1cnc[nH][]1[])C([]=[]O)N[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txt t/m/n/10 ](CCCNC([]=[]N)N)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/ 10 ](Cc1c[nH]c3ccccc13)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCCNC([]=[]N)N)C([]=[]O)N2| Overfull \hbox (149.74318pt too wide) in paragraph at lines 11596--11596 []\T1/txtt/m/n/10 CN1C([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCCNC( []=[]N)N)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccc(O)cc2 )NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O)[C []\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccc3ccccc3c2)NC([]=[]O)[C[]@[][]\T1 /txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]CC([]=[]O)O| Overfull \hbox (97.24333pt too wide) in paragraph at lines 11597--11597 []\T1/txtt/m/n/10 NCCCC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](NC([]=[]O)[C[ ]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1ccc(OP([]=[]O)(O)O)cc1)NC([]=[]O)Cc1 ccccc1)C([]=[]O)N1CCC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]C([]=[]O)N[ C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1ccccc1)C(N)[]=[]O| Overfull \hbox (643.24174pt too wide) in paragraph at lines 11598--11598 []\T1/txtt/m/n/10 CCCCCCCCCCCCCCCCNC([]=[]O)CN(CC([]=[]O)NC(C)(C)C([]=[]O)N[C[] @[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/tx tt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC(C)C)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[ ]\T1/txtt/m/n/10 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m /n/10 ](CCCNC([]=[]N)N)C([]=[]O)N1CCC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ] []1[]C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCCNC([]=[]N)N)C ([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC(N)[]=[]O)C(N)[]=[]O )C([]=[]O)c1cccnc1| Overfull \hbox (359.74257pt too wide) in paragraph at lines 11599--11599 []\T1/txtt/m/n/10 CC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)[C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/tx tt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC(C )C)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O) [C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt/bx/ n/10 @H[]\T1/txtt/m/n/10 ](C(C)C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/ n/10 ](CC(C)C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCSC)NC1[]=[ ]O| Overfull \hbox (370.24254pt too wide) in paragraph at lines 11600--11600 []\T1/txtt/m/n/10 CC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)[C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/tx tt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC(C )C)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O) [C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt/bx/ n/10 @H[]\T1/txtt/m/n/10 ](C(C)C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/ n/10 ](CC(C)C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC[S[]+[]](C )[O[]- Overfull \hbox (422.74239pt too wide) in paragraph at lines 11601--11601 []\T1/txtt/m/n/10 CC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)[C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/tx tt/m/n/10 ](Cc2c[nH]c3ccccc23)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/1 0 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccccc2)NC ([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O)[C[]\ T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCSC)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\ T1/txtt/m/n/10 ](CC(C)C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC [S[]+[]](C)[O[]- Overfull \hbox (249.49289pt too wide) in paragraph at lines 11602--11602 [][]\T1/txtt/m/n/10 ])NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C(C) C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2c[nH]c3ccccc23)NC([]= []O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt /bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H []\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC[S[]+[]](C)[O[]- Overfull \hbox (522.4921pt too wide) in paragraph at lines 11603--11603 []\T1/txtt/m/n/10 CC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)[C[]\T1/txtt/b x/n/10 @H[]\T1/txtt/m/n/10 ](N)C([]=[]O)N[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/ 10 ](C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC(C)C)C([]=[]O) N[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C([]=[]O)N1CCC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]C([]=[]O)N1CCC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/1 0 ][]1[]C([]=[]O)N[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCC([]=[]O)N[C[]@[ ][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCC([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC(C)C)C([]=[]O)O)Cc1ccccc1)Cc1ccccc1)C(C)C)[C[]@[][]\T1 /txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)CC| Overfull \vbox (3.1787pt too high) detected at line 11607 [130] [131] [132] [133] [134] [135] Overfull \vbox (2.67389pt too high) detected at line 11966 [136] [137] [138] [139] [140] [141] [142] [143] [144] Chapter 6. [145] [146] Underfull \hbox (badness 10000) in paragraph at lines 12751--12755 \T1/qtm/m/n/10 Un-charger::uncharge() will now neu-tral-ize \T1/txtt/m/n/10 [Cl ,Br,I][O[]], [Cl,Br,I](=O)[O[]], [Cl, Underfull \hbox (badness 10000) in paragraph at lines 12751--12755 \T1/txtt/m/n/10 Br,I](=O)(=O)[O[]], [Cl,Br,I](=O)(=O)(=O)[O[]], [O[]]N=N[O[]], [N,P](=O)[O[]], Underfull \hbox (badness 10000) in paragraph at lines 12751--12755 \T1/txtt/m/n/10 [N+](=O)([O[]])[O[]], P(=O)([O[]])[O[]], P(=O)([O[]])([O[]])[O[ ]], S([O[]])[O[]], S(=O)([O[]])[O[]], [147] [148] [149] [150] Chapter 7. [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] Chapter 8. [169] [170] [171] Underfull \hbox (badness 10000) in paragraph at lines 14914--14918 \T1/qtm/m/n/10 Groups of molecules are read us-ing a Sup-plier (for ex-am-ple, an \T1/txtt/m/n/10 RDKit::SDMolSupplier \T1/qtm/m/n/10 or an [172] [173] [174] [175] [176] [177] [178] Underfull \hbox (badness 6691) in paragraph at lines 15454--15456 []\T1/qtm/m/n/10 The \T1/txtt/m/n/10 auto\TS1/txtt/m/n/10 ' \T1/txtt/m/n/10 key word here is hiding the fact that \T1/qtm/m/n/10 get-Bond-Be-tweenAtoms\T1/txtt /m/n/10 returns the index of the [179] [180] LaTeX Warning: Hyper reference `GettingStartedInC++:TheSSSRProblem' on page 181 undefined on input line 15582. LaTeX Warning: Hyper reference `GettingStartedInC++:twoAddHs' on page 181 undef ined on input line 15612. [181] [182] Overfull \vbox (1.27959pt too high) detected at line 15784 [183] LaTeX Warning: Hyper reference `GettingStartedInC++:blaney' on page 184 undefin ed on input line 15802. LaTeX Warning: Hyper reference `GettingStartedInC++:rappe' on page 184 undefine d on input line 15837. LaTeX Warning: Hyper reference `GettingStartedInC++:riniker2' on page 184 undef ined on input line 15841. [184] LaTeX Warning: Hyper reference `GettingStartedInC++:mmff1' on page 185 undefine d on input line 15885. LaTeX Warning: Hyper reference `GettingStartedInC++:mmff2' on page 185 undefine d on input line 15885. LaTeX Warning: Hyper reference `GettingStartedInC++:mmff3' on page 185 undefine d on input line 15885. LaTeX Warning: Hyper reference `GettingStartedInC++:mmff4' on page 185 undefine d on input line 15886. LaTeX Warning: Hyper reference `GettingStartedInC++:mmffs' on page 185 undefine d on input line 15886. [185] [186] [187] [188] [189] Overfull \vbox (0.52191pt too high) detected at line 16321 [190] [191] LaTeX Warning: Hyper reference `GettingStartedInC++:guba' on page 192 undefined on input line 16440. [192] [193] [194] Chapter 9. [195] [196] Chapter 10. (./RDKit.ind) [197] (./RDKit.aux) LaTeX Warning: There were undefined references. ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ec.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r .enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc} Output written on RDKit.pdf (205 pages, 1860330 bytes). Transcript written on RDKit.log. Latexmk: Getting log file 'RDKit.log' Latexmk: Examining 'RDKit.fls' Latexmk: Examining 'RDKit.log' Latexmk: Index file 'RDKit.idx' was written Latexmk: Log file says output to 'RDKit.pdf' Latexmk: applying rule 'pdflatex'... 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[17] [18] [19] [20] [21] [22] [23] [24] [25] [26] Underfull \hbox (badness 10000) in paragraph at lines 1978--1981 []\T1/qtm/m/n/10 An-other op-tion for Com-pute2DCoords al-lows you to gen-er-at e 2D de-pic-tions for molecules that Underfull \hbox (badness 10000) in paragraph at lines 1978--1981 \T1/qtm/m/n/10 closely mimic 3D con-form-ers. This is avail-able us-ing the fun c-tion \T1/txtt/m/n/10 rdkit.Chem.AllChem. Underfull \hbox (badness 10000) in paragraph at lines 2003--2009 []\T1/qtm/m/n/10 More fine-grained con-trol can be ob-tained us-ing the core fu nc-tion \T1/txtt/m/n/10 rdkit.Chem.rdDepictor. 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[81 <./picture_9.png (PNG copy)>] [82 <./picture_8.png> <./picture_7.png (PNG c opy)>] [83 <./picture_10.png> <./picture_12.png>] [84 <./picture_11.png>] [85] [86] [87] [88] [89] [90] [91] [92 <./parastereo_2.png> <./parastereo_1.png >] [93 <./potential_stereo_double_bond1.png> <./potential_stereo_double_bond2.p ng> <./potential_stereo_double_bond3.png>] [94] [95] [96 <./nontetstereo_sp1.pn g> <./nontetstereo_sp2.png> <./nontetstereo_sp3.png> <./nontetstereo_sp4.png> < ./nontetstereo_tb2.png>] [97 <./nontetstereo_tb1.png> <./nontetstereo_oh2.png>] [98 <./nontetstereo_oh1.png>] Underfull \hbox (badness 10000) in paragraph at lines 8891--8893 []\T1/qtm/m/n/10 The clas-sic ex-am-ple of this is cis-platin - \T1/txtt/m/n/10 Cl[Pt@SP1](Cl)(<[][NH3])<[][NH3] \T1/qtm/m/n/10 - vs trans-platin - [99 <./nontetstereo_ex1.png> <./nontetstereo_ex2.png> <./nontetstereo_missing1. png>] [100] [101] [102] [103] [104] [105] [106] [107 <./picture_10.jpg>] [108] [109 <./ary_group.png>] [110] Underfull \hbox (badness 10000) in paragraph at lines 10183--10183 []\T1/qtm/m/n/10 _Chi-ral-i-ty-Pos-si- Underfull \hbox (badness 10000) in paragraph at lines 10183--10183 []\T1/qtm/m/n/10 _Re-ac-tion-De- Underfull \hbox (badness 10000) in paragraph at lines 10183--10183 []\T1/qtm/m/n/10 mo-lAtomMap- Underfull \hbox (badness 10000) in paragraph at lines 10183--10183 []\T1/qtm/m/n/10 molFileIn-ver- Underfull \hbox (badness 10000) in paragraph at lines 10183--10183 []\T1/qtm/m/n/10 mol-Rxn-Com-po- [111] [112] [113] Underfull \hbox (badness 10000) in paragraph at lines 10345--10350 []\T1/qtm/m/n/10 By de-fault the \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles.SDMolSup plier \T1/qtm/m/n/10 and \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles. Underfull \hbox (badness 10000) in paragraph at lines 10394--10397 []\T1/qtm/m/n/10 This be-hav-ior is en-abled by de-fault and can be turned on/o ff with the \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles. Underfull \hbox (badness 10000) in paragraph at lines 10398--10402 \T1/qtm/m/n/10 tions \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles.CreateAtomStringProp ertyList()\T1/qtm/m/n/10 , \T1/txtt/m/n/10 rdkit.Chem.rdmolfiles. [114] Underfull \hbox (badness 10000) in paragraph at lines 10542--10542 []\T1/qhv/m/n/10 Mix- Underfull \hbox (badness 10000) in paragraph at lines 10542--10542 []\T1/qtm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 10542--10542 []\T1/qtm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 10542--10542 []\T1/qtm/m/n/10 mix- Underfull \hbox (badness 10000) in paragraph at lines 10542--10542 []\T1/qtm/m/n/10 mix- [115] [116 <./enhanced_stereo_and1_and2_base.png> <./enhanced_stereo_and1_and2_ expand.png> <./enhanced_stereo_and1_cis_base.png> <./enhanced_stereo_and1_cis_e xpand.png> <./enhanced_stereo_and1_trans_base.png> <./enhanced_stereo_and1_tran s_expand.png> <./enhanced_stereo_or1_or2_base.png> <./enhanced_stereo_or1_cis_b ase.png> <./enhanced_stereo_or1_trans_base.png> <./enhanced_stereo_abs_and_base .png> <./enhanced_stereo_abs_and_expand.png> <./enhanced_stereo_abs_or_base.png >] Underfull \hbox (badness 10000) in paragraph at lines 10559--10562 []\T1/qtm/m/n/10 It is pos-si-ble to enu-mer-ate the el-e-ments of a \T1/txtt/m /n/10 StereoGroup \T1/qtm/m/n/10 us-ing the func-tion \T1/txtt/m/n/10 rdkit.Che m. [117] [118 <./EnhancedStereoSSS_molA.png> <./EnhancedStereoSSS_molB.png> <./Enh ancedStereoSSS_molC.png> <./EnhancedStereoSSS_molD.png> <./EnhancedStereoSSS_mo lE.png> <./EnhancedStereoSSS_molF.png> <./EnhancedStereoSSS_molG.png>] [119 <./ query_bonds.png>] [120 <./query_bonds.2.png> <./query_atoms.png>] [121] [122] [123] Underfull \hbox (badness 10000) in paragraph at lines 11247--11257 []\T1/txtt/m/n/10 allowNontetrahedralChirality\T1/qtm/m/n/10 : when this is \T1 /txtt/m/n/10 true \T1/qtm/m/n/10 non-tetrahedral chi-ral-ity will be per- Underfull \hbox (badness 10000) in paragraph at lines 11247--11257 \T1/qtm/m/n/10 ceived from 3D co-or-di-nates. The de-fault value is \T1/txtt/m/ n/10 true \T1/qtm/m/n/10 un-less the en-vi-ron-ment vari- Underfull \hbox (badness 10000) in paragraph at lines 11247--11257 \T1/qtm/m/n/10 able \T1/txtt/m/n/10 RDK_ENABLE_NONTETRAHEDRAL_STEREO \T1/qtm/m/ n/10 is set to \T1/txtt/m/n/10 "0"\T1/qtm/m/n/10 . Can set/checked from Underfull \hbox (badness 10000) in paragraph at lines 11247--11257 \T1/qtm/m/n/10 C++ us-ing the func-tions \T1/txtt/m/n/10 RDKit::Chirality::setA llowNontetrahedralChirality() \T1/qtm/m/n/10 / Underfull \hbox (badness 10000) in paragraph at lines 11247--11257 \T1/txtt/m/n/10 RDKit::Chirality::getAllowNontetrahedralChirality() \T1/qtm/m/n /10 or from Python us-ing the func-tions Underfull \hbox (badness 10000) in paragraph at lines 11259--11269 []\T1/txtt/m/n/10 useLegacyStereoPerception\T1/qtm/m/n/10 : when this is \T1/tx tt/m/n/10 true \T1/qtm/m/n/10 the legacy im-ple-men-ta-tion for per- Underfull \hbox (badness 10000) in paragraph at lines 11259--11269 \T1/qtm/m/n/10 ceiv-ing stere-o-chem-istry will be used. The de-fault value is \T1/txtt/m/n/10 true \T1/qtm/m/n/10 un-less the en-vi-ron- Underfull \hbox (badness 10000) in paragraph at lines 11259--11269 \T1/qtm/m/n/10 ment vari-able \T1/txtt/m/n/10 RDK_USE_LEGACY_STEREO_PERCEPTION \T1/qtm/m/n/10 is set to \T1/txtt/m/n/10 "0"\T1/qtm/m/n/10 . Can set/checked Underfull \hbox (badness 10000) in paragraph at lines 11259--11269 \T1/qtm/m/n/10 from C++ us-ing the func-tions \T1/txtt/m/n/10 RDKit::Chirality: :setUseLegacyStereoPerception() \T1/qtm/m/n/10 / [124] Chapter 5. [125] [126] [127] [128] [129] Overfull \hbox (1052.74055pt too wide) in paragraph at lines 11571--11571 []\T1/txtt/m/n/10 CC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)[C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\ T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/1 0 ][]2[]CCCN2C([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ]([C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)CC)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/t xtt/m/n/10 ](CO)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)NC([]=[] O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ]([C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/ m/n/10 ](C)O)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CSSC [C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](NC1[]=[]O)C([]=[]O)N[C[]@[][]\T1/txt t/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1cnc[nH][]1[])C([]=[]O)N[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txt t/m/n/10 ](CCCNC([]=[]N)N)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/ 10 ](Cc1c[nH]c3ccccc13)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCCNC([]=[]N)N)C([]=[]O)N2| Overfull \hbox (149.74318pt too wide) in paragraph at lines 11573--11573 []\T1/txtt/m/n/10 CN1C([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCCNC( []=[]N)N)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccc(O)cc2 )NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O)[C []\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccc3ccccc3c2)NC([]=[]O)[C[]@[][]\T1 /txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]CC([]=[]O)O| Overfull \hbox (97.24333pt too wide) in paragraph at lines 11574--11574 []\T1/txtt/m/n/10 NCCCC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](NC([]=[]O)[C[ ]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1ccc(OP([]=[]O)(O)O)cc1)NC([]=[]O)Cc1 ccccc1)C([]=[]O)N1CCC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]C([]=[]O)N[ C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1ccccc1)C(N)[]=[]O| Overfull \hbox (643.24174pt too wide) in paragraph at lines 11575--11575 []\T1/txtt/m/n/10 CCCCCCCCCCCCCCCCNC([]=[]O)CN(CC([]=[]O)NC(C)(C)C([]=[]O)N[C[] @[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/tx tt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC(C)C)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[ ]\T1/txtt/m/n/10 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m /n/10 ](CCCNC([]=[]N)N)C([]=[]O)N1CCC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ] []1[]C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCCNC([]=[]N)N)C ([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC(N)[]=[]O)C(N)[]=[]O )C([]=[]O)c1cccnc1| Overfull \hbox (464.74226pt too wide) in paragraph at lines 11576--11576 []\T1/txtt/m/n/10 CCCCCCCCCCCCCCCCN(CCCCCCCCCCCCCCCC)CCCCCC([]=[]O)NC(C)(C)C([] =[]O)NC(Cc1ccccc1)C([]=[]O)NC(CC(C)C)C([]=[]O)NC(Cc1ccccc1)C([]=[]O)NC(CCCNC([] =[]N)N)C([]=[]O)N1CCCC1C([]=[]O)NC(CCCNC([]=[]N)N)C([]=[]O)NC(CC(N)[]=[]O)C(N)[ ]=[]O| Overfull \hbox (359.74257pt too wide) in paragraph at lines 11577--11577 []\T1/txtt/m/n/10 CC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)[C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/tx tt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC(C )C)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O) [C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt/bx/ n/10 @H[]\T1/txtt/m/n/10 ](C(C)C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/ n/10 ](CC(C)C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCSC)NC1[]=[ ]O| Overfull \hbox (370.24254pt too wide) in paragraph at lines 11578--11578 []\T1/txtt/m/n/10 CC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)[C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/tx tt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC(C )C)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O) [C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt/bx/ n/10 @H[]\T1/txtt/m/n/10 ](C(C)C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/ n/10 ](CC(C)C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC[S[]+[]](C )[O[]- Overfull \hbox (422.74239pt too wide) in paragraph at lines 11579--11579 []\T1/txtt/m/n/10 CC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)[C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/tx tt/m/n/10 ](Cc2c[nH]c3ccccc23)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/1 0 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccccc2)NC ([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O)[C[]\ T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCSC)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\ T1/txtt/m/n/10 ](CC(C)C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC [S[]+[]](C)[O[]- Overfull \hbox (249.49289pt too wide) in paragraph at lines 11580--11580 [][]\T1/txtt/m/n/10 ])NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C(C) C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2c[nH]c3ccccc23)NC([]= []O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt /bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H []\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC[S[]+[]](C)[O[]- Overfull \hbox (1052.74055pt too wide) in paragraph at lines 11594--11594 []\T1/txtt/m/n/10 CC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)[C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\ T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/1 0 ][]2[]CCCN2C([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ]([C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)CC)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/t xtt/m/n/10 ](CO)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)NC([]=[] O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ]([C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/ m/n/10 ](C)O)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CSSC [C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](NC1[]=[]O)C([]=[]O)N[C[]@[][]\T1/txt t/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1cnc[nH][]1[])C([]=[]O)N[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txt t/m/n/10 ](CCCNC([]=[]N)N)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/ 10 ](Cc1c[nH]c3ccccc13)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCCNC([]=[]N)N)C([]=[]O)N2| Overfull \hbox (149.74318pt too wide) in paragraph at lines 11596--11596 []\T1/txtt/m/n/10 CN1C([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCCNC( []=[]N)N)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccc(O)cc2 )NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O)[C []\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccc3ccccc3c2)NC([]=[]O)[C[]@[][]\T1 /txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]CC([]=[]O)O| Overfull \hbox (97.24333pt too wide) in paragraph at lines 11597--11597 []\T1/txtt/m/n/10 NCCCC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](NC([]=[]O)[C[ ]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1ccc(OP([]=[]O)(O)O)cc1)NC([]=[]O)Cc1 ccccc1)C([]=[]O)N1CCC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]C([]=[]O)N[ C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1ccccc1)C(N)[]=[]O| Overfull \hbox (643.24174pt too wide) in paragraph at lines 11598--11598 []\T1/txtt/m/n/10 CCCCCCCCCCCCCCCCNC([]=[]O)CN(CC([]=[]O)NC(C)(C)C([]=[]O)N[C[] @[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/tx tt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC(C)C)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[ ]\T1/txtt/m/n/10 ](Cc1ccccc1)C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m /n/10 ](CCCNC([]=[]N)N)C([]=[]O)N1CCC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ] []1[]C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCCNC([]=[]N)N)C ([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC(N)[]=[]O)C(N)[]=[]O )C([]=[]O)c1cccnc1| Overfull \hbox (359.74257pt too wide) in paragraph at lines 11599--11599 []\T1/txtt/m/n/10 CC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)[C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/tx tt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC(C )C)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O) [C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt/bx/ n/10 @H[]\T1/txtt/m/n/10 ](C(C)C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/ n/10 ](CC(C)C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCSC)NC1[]=[ ]O| Overfull \hbox (370.24254pt too wide) in paragraph at lines 11600--11600 []\T1/txtt/m/n/10 CC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)[C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/tx tt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC(C )C)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O) [C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt/bx/ n/10 @H[]\T1/txtt/m/n/10 ](C(C)C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/ n/10 ](CC(C)C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC[S[]+[]](C )[O[]- Overfull \hbox (422.74239pt too wide) in paragraph at lines 11601--11601 []\T1/txtt/m/n/10 CC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)[C[]@[][]\T1/t xtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/tx tt/m/n/10 ](Cc2c[nH]c3ccccc23)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/1 0 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccccc2)NC ([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O)[C[]\ T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCSC)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\ T1/txtt/m/n/10 ](CC(C)C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC [S[]+[]](C)[O[]- Overfull \hbox (249.49289pt too wide) in paragraph at lines 11602--11602 [][]\T1/txtt/m/n/10 ])NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C(C) C)NC([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2c[nH]c3ccccc23)NC([]= []O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]\T1/txtt /bx/n/10 @H[]\T1/txtt/m/n/10 ](Cc2ccccc2)NC([]=[]O)[C[]@[][]\T1/txtt/bx/n/10 @H []\T1/txtt/m/n/10 ][]2[]CCCN2C([]=[]O)[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC[S[]+[]](C)[O[]- Overfull \hbox (522.4921pt too wide) in paragraph at lines 11603--11603 []\T1/txtt/m/n/10 CC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)[C[]\T1/txtt/b x/n/10 @H[]\T1/txtt/m/n/10 ](N)C([]=[]O)N[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/ 10 ](C([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC(C)C)C([]=[]O) N[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C([]=[]O)N1CCC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ][]1[]C([]=[]O)N1CCC[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/1 0 ][]1[]C([]=[]O)N[C[]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCC([]=[]O)N[C[]@[ ][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CCC([]=[]O)N[C[]@[][]\T1/txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](CC(C)C)C([]=[]O)O)Cc1ccccc1)Cc1ccccc1)C(C)C)[C[]@[][]\T1 /txtt/bx/n/10 @H[]\T1/txtt/m/n/10 ](C)CC| Overfull \vbox (3.1787pt too high) detected at line 11607 [130] [131] [132] [133] [134] [135] Overfull \vbox (2.67389pt too high) detected at line 11966 [136] [137] [138] [139] [140] [141] [142] [143] [144] Chapter 6. [145] [146] Underfull \hbox (badness 10000) in paragraph at lines 12751--12755 \T1/qtm/m/n/10 Un-charger::uncharge() will now neu-tral-ize \T1/txtt/m/n/10 [Cl ,Br,I][O[]], [Cl,Br,I](=O)[O[]], [Cl, Underfull \hbox (badness 10000) in paragraph at lines 12751--12755 \T1/txtt/m/n/10 Br,I](=O)(=O)[O[]], [Cl,Br,I](=O)(=O)(=O)[O[]], [O[]]N=N[O[]], [N,P](=O)[O[]], Underfull \hbox (badness 10000) in paragraph at lines 12751--12755 \T1/txtt/m/n/10 [N+](=O)([O[]])[O[]], P(=O)([O[]])[O[]], P(=O)([O[]])([O[]])[O[ ]], S([O[]])[O[]], S(=O)([O[]])[O[]], [147] [148] [149] [150] Chapter 7. [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] Chapter 8. [169] [170] [171] Underfull \hbox (badness 10000) in paragraph at lines 14914--14918 \T1/qtm/m/n/10 Groups of molecules are read us-ing a Sup-plier (for ex-am-ple, an \T1/txtt/m/n/10 RDKit::SDMolSupplier \T1/qtm/m/n/10 or an [172] [173] [174] [175] [176] [177] [178] Underfull \hbox (badness 6691) in paragraph at lines 15454--15456 []\T1/qtm/m/n/10 The \T1/txtt/m/n/10 auto\TS1/txtt/m/n/10 ' \T1/txtt/m/n/10 key word here is hiding the fact that \T1/qtm/m/n/10 get-Bond-Be-tweenAtoms\T1/txtt /m/n/10 returns the index of the [179] [180] LaTeX Warning: Hyper reference `GettingStartedInC++:TheSSSRProblem' on page 181 undefined on input line 15582. LaTeX Warning: Hyper reference `GettingStartedInC++:twoAddHs' on page 181 undef ined on input line 15612. [181] [182] Overfull \vbox (1.27959pt too high) detected at line 15784 [183] LaTeX Warning: Hyper reference `GettingStartedInC++:blaney' on page 184 undefin ed on input line 15802. LaTeX Warning: Hyper reference `GettingStartedInC++:rappe' on page 184 undefine d on input line 15837. LaTeX Warning: Hyper reference `GettingStartedInC++:riniker2' on page 184 undef ined on input line 15841. [184] LaTeX Warning: Hyper reference `GettingStartedInC++:mmff1' on page 185 undefine d on input line 15885. LaTeX Warning: Hyper reference `GettingStartedInC++:mmff2' on page 185 undefine d on input line 15885. LaTeX Warning: Hyper reference `GettingStartedInC++:mmff3' on page 185 undefine d on input line 15885. LaTeX Warning: Hyper reference `GettingStartedInC++:mmff4' on page 185 undefine d on input line 15886. LaTeX Warning: Hyper reference `GettingStartedInC++:mmffs' on page 185 undefine d on input line 15886. [185] [186] [187] [188] [189] Overfull \vbox (0.52191pt too high) detected at line 16321 [190] [191] LaTeX Warning: Hyper reference `GettingStartedInC++:guba' on page 192 undefined on input line 16440. [192] [193] [194] Chapter 9. [195] [196] Chapter 10. (./RDKit.ind) [197] (./RDKit.aux) LaTeX Warning: There were undefined references. ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ec.enc}{/usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r .enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc} Output written on RDKit.pdf (205 pages, 1860330 bytes). Transcript written on RDKit.log. Latexmk: Getting log file 'RDKit.log' Latexmk: Examining 'RDKit.fls' Latexmk: Examining 'RDKit.log' Latexmk: Index file 'RDKit.idx' was written Latexmk: Log file says output to 'RDKit.pdf' Latexmk: All targets () are up-to-date make[3]: Leaving directory '/build/reproducible-path/rdkit-202209.3/Docs/Book/_build/latex' pdflatex finished; the PDF files are in _build/latex. make[2]: Leaving directory '/build/reproducible-path/rdkit-202209.3/Docs/Book' make[1]: Leaving directory '/build/reproducible-path/rdkit-202209.3' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/rdkit-202209.3' cp -r rdkit obj-*/ find /build/reproducible-path/rdkit-202209.3 -name rdchem.so /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 -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 -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. 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 Test project /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: testCoordGen 1: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/CoordGen/testCoordGen 1: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/CoordGen 1: Test timeout computed to be: 1500 test 2 Start 2: pyCoordGen 2: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/External/CoordGen/Wrap/testCoordGen.py" 2: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/External/CoordGen/Wrap 2: Test timeout computed to be: 1500 test 3 Start 3: testDict 3: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral/testDict 3: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral 3: Test timeout computed to be: 1500 test 4 Start 4: testRDValue 4: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral/testRDValue 4: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral 4: Test timeout computed to be: 1500 test 5 Start 5: testConcurrentQueue 5: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral/testConcurrentQueue 5: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral 5: Test timeout computed to be: 1500 test 6 Start 6: dictTestsCatch 6: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral/dictTestsCatch 6: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/RDGeneral 6: Test timeout computed to be: 1500 test 7 Start 7: logTestsCatch 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 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 3: dict get int vect 4: -- running tests -- 4: min: -2147483648 -2147483648 4: min: 0 0 4: min: 2.22507e-308 2.22507e-308 4: min: 1.17549e-38 1.17549e-38 4: min: 0 0 4: == int 4: == double 4: == float 4: == unsigned int 4: == bool 4: == std::string 5: [16:02:52] 5: ----------------------------------------- 5: [16:02:52] Finished: testPushAndPop() 5: [16:02:52] 5: ----------------------------------------- 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: 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, 8: t1|t2: 10, 11, 14, 15, 17, 8: t1&t2: 10, 11, 8: t1^t2: 14, 15, 17, 8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, 8: except 8: 10, 11, 14, 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, 8: t1&t2: 10, 11, 8: t1^t2: 14, 15, 17, 8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, 8: except 4/208 Test #9: testFPB ................................ Passed 0.03 sec 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 5/208 Test #8: testDataStructs ........................ Passed 0.05 sec 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 6/208 Test #10: testMultiFPB ........................... Passed 0.05 sec 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 1: core 1: RDKit 2D 1: 1: 4 4 0 0 0 0 0 0 0 0999 V2000 1: 0.6824 0.1850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.1850 -0.6824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.6824 -0.1850 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1850 0.6824 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 1 1 0 1: M END 1: 1: core+sidechain 1: RDKit 2D 1: 1: 7 7 0 0 0 0 0 0 0 0999 V2000 1: 0.6496 0.9080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3926 -0.0584 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4726 -0.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.3396 -0.0616 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.2048 -0.5634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.3590 -0.3156 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.6160 0.6508 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 2 6 1 0 1: 6 7 1 0 1: 7 1 1 0 1: M END 1: 1: templated 1: RDKit 2D 1: 1: 7 7 0 0 0 0 0 0 0 0999 V2000 1: 0.6824 0.1850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.1850 -0.6824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.6824 -0.1850 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1850 0.6824 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 2 6 1 0 1: 6 7 1 0 1: 7 1 1 0 1: M END 1: 1: core 1: RDKit 2D 1: 1: 10 10 0 0 0 0 0 0 0 0999 V2000 1: -1.2956 -1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2984 -0.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4338 0.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4366 1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4280 1.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2956 1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2984 0.2536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4338 -0.2488 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4366 -1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4280 -1.7512 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 1 1 0 1: M END 1: 1: core+sidechain 1: RDKit 2D 1: 1: 12 12 0 0 0 0 0 0 0 0999 V2000 1: 0.2846 -0.7516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2790 -1.7516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5898 -2.2466 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4530 -1.7418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4476 -0.7418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5788 -0.2468 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5732 0.7532 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2956 1.2484 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3012 2.2482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.1700 2.7434 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.1590 0.7434 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.1534 -0.2564 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 8 11 1 0 1: 11 12 1 0 1: 12 1 1 0 1: M END 1: 1: templated 1: RDKit 2D 1: 1: 12 12 0 0 0 0 0 0 0 0999 V2000 1: -1.2984 -0.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4338 0.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4366 1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4280 1.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2956 1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2984 0.2536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4338 -0.2488 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4366 -1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4280 -1.7512 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2956 -1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 8 11 1 0 1: 11 12 1 0 1: 12 1 1 0 1: M END 1: 1: core 1: RDKit 2D 1: 1: 10 10 0 0 0 0 0 0 0 0999 V2000 1: -1.2956 -1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2984 -0.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4338 0.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4366 1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4280 1.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2956 1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2984 0.2536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4338 -0.2488 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4366 -1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4280 -1.7512 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 1 1 0 1: M END 1: 1: core+sidechain 1: RDKit 2D 1: 1: 16 16 0 0 0 0 0 0 0 0999 V2000 1: 1.7868 0.7799 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.6532 1.2791 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.5187 0.7785 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.5180 -0.2215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.6515 -0.7209 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.7860 -0.2201 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.9195 -0.7195 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0539 -0.2189 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8124 -0.7181 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.6780 -0.2175 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.5445 -0.7167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.4101 -0.2161 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.2764 -0.7153 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.1421 -0.2147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0547 0.7811 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.9211 1.2805 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 1 0 1: 11 12 1 0 1: 12 13 1 0 1: 13 14 1 0 1: 8 15 1 0 1: 15 16 1 0 1: 16 1 1 0 1: M END 1: 1: templated 1: RDKit 2D 1: 1: 16 16 0 0 0 0 0 0 0 0999 V2000 1: -1.2984 -0.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4338 0.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4366 1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4280 1.7512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2956 1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2984 0.2536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4338 -0.2488 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.4366 -1.2488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4280 -1.7512 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2956 -1.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 1 0 1: 11 12 1 0 1: 12 13 1 0 1: 13 14 1 0 1: 8 15 1 0 1: 15 16 1 0 1: 16 1 1 0 1: M END 1: 1: core 1: RDKit 2D 1: 1: 9 10 0 0 0 0 0 0 0 0999 V2000 1: 0.6718 -0.9994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5374 -0.4988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5366 0.5012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6702 1.0006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1954 0.4998 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1946 -0.5002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1454 -0.8098 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.7338 -0.0014 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1466 0.8082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 6 1 1 0 1: 9 5 1 0 1: M END 1: 1: core+sidechain 1: RDKit 2D 1: 1: 19 21 0 0 0 0 0 0 0 0999 V2000 1: -0.5657 -0.9286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4321 -0.4294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.2977 -0.9300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.2969 -1.9300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.1625 -2.4306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4329 0.5708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5673 1.0714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5681 2.0714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2975 2.5720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2975 2.5728 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.7969 3.4386 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2991 0.5720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.2999 -0.4278 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2513 -0.7362 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5609 -1.6870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.5393 -1.8942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.8923 -2.4306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.8381 0.0734 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2499 0.8820 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 2 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 1 0 1: 7 12 1 0 1: 12 13 1 0 1: 13 14 1 0 1: 14 15 1 0 1: 15 16 1 0 1: 15 17 1 0 1: 14 18 1 0 1: 18 19 1 0 1: 13 1 1 0 1: 19 12 1 0 1: 11 9 1 0 1: M END 1: 1: templated 1: RDKit 2D 1: 1: 19 21 0 0 0 0 0 0 0 0999 V2000 1: 0.5360 -0.9365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4021 -0.4366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.2680 -0.9366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.2680 -1.9366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4020 -2.4366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4021 0.5634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5360 1.0633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5360 2.0634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.3300 2.5633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.3300 2.5633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8300 3.4295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.3300 0.5634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.3300 -0.4366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2812 -0.7457 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.5900 -1.6966 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.9208 -2.4398 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.5682 -1.9046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.8686 0.0634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.2812 0.8725 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 2 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 1 0 1: 7 12 1 0 1: 12 13 1 0 1: 13 14 1 0 1: 14 15 1 0 1: 15 16 1 0 1: 15 17 1 0 1: 14 18 1 0 1: 18 19 1 0 1: 13 1 1 0 1: 19 12 1 0 1: 11 9 1 0 1: M END 1: 1: core 1: RDKit 2D 1: 1: 5 4 0 0 0 0 0 0 0 0999 V2000 1: 1.2134 -0.4976 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: 0.3444 1.0006 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.5186 -0.5010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.3856 -0.0028 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: M END 1: 1: core+sidechain 1: RDKit 2D 1: 1: 7 6 0 0 0 0 0 0 0 0999 V2000 1: -1.7333 -0.5679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8661 -0.0697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8641 0.9303 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 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: 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 0.018s 12: 12: OK 13: ......... 13: ---------------------------------------------------------------------- 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: 1: 85 85 0 0 0 0 0 0 0 0999 V2000 1: 1.4840 -0.8529 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6174 -1.3521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6176 -2.3509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4860 -2.8479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4912 -3.8489 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.3504 -2.3385 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.3352 -1.3311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.1902 -0.7993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.1580 0.1961 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.0642 -1.2607 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.9260 -0.7295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.9144 0.3303 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 5.7766 0.8337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.0008 0.8409 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.8596 1.9125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.8162 2.2071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.2038 1.4219 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.2560 3.1855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.5280 4.2325 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.7128 4.8927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.8530 5.8895 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.7676 4.5077 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.0820 5.0835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.9744 4.6151 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.8344 5.1337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.9792 3.6203 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.8192 3.0813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.7974 3.5817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.7998 4.5809 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.7790 3.0789 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.8812 2.0705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.1202 1.6017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.4194 2.0931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.0590 0.6211 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.8626 0.0983 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.8096 -0.8961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.6470 -1.4375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.9122 -1.3587 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.8776 -2.3565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.9982 -2.8425 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1382 -2.3311 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.9886 -3.8459 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1202 -4.3461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.2526 -3.8491 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6116 -4.3521 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.2494 -2.8505 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.1228 -5.3475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.2584 -5.8507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6092 -5.3541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.2624 -6.8511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6018 -7.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5982 -8.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.4624 -8.8579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.9906 -5.8449 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.8520 -4.3501 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.7288 -2.8719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.7098 -3.8701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.6032 -2.3871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.0646 -0.8235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.7362 0.5679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.5794 0.0605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.5618 -0.9361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -6.4498 0.5487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.1626 0.1727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.7698 1.6253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.5952 2.1745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -6.4896 1.7311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.5292 3.1711 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.6054 3.6407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.7186 2.0867 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.0328 6.0847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.4396 4.6417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.4580 5.6909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.3220 6.1985 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.5836 6.2065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.2682 3.0557 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.6630 2.5215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.5648 3.5065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 5.5876 2.1073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 5.7968 -1.2481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 6.6784 -0.7913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 7.5218 -1.3355 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 6.7252 0.2017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.0970 -2.2659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.2220 -2.8307 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 3 2 1 1 1: 3 4 1 0 1: 4 5 2 0 1: 4 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 2 0 1: 8 10 1 0 1: 10 11 1 0 1: 11 12 1 0 1: 12 13 2 0 1: 12 14 1 0 1: 14 15 1 0 1: 15 16 1 0 1: 16 17 2 0 1: 16 18 1 0 1: 18 19 1 0 1: 19 20 1 0 1: 20 21 2 0 1: 20 22 1 0 1: 22 23 1 0 1: 23 24 1 0 1: 24 25 2 0 1: 24 26 1 0 1: 26 27 1 0 1: 27 28 1 0 1: 28 29 2 0 1: 28 30 1 0 1: 30 31 1 0 1: 31 32 1 0 1: 32 33 2 0 1: 32 34 1 0 1: 34 35 1 0 1: 35 36 1 0 1: 36 37 2 0 1: 36 38 1 0 1: 38 39 1 0 1: 39 40 1 0 1: 40 41 2 0 1: 40 42 1 0 1: 43 42 1 6 1: 43 44 1 0 1: 44 45 2 0 1: 44 46 1 0 1: 43 47 1 0 1: 47 48 1 0 1: 48 49 1 6 1: 48 50 1 0 1: 50 51 1 0 1: 51 52 2 0 1: 52 53 1 0 1: 47 54 1 1 1: 42 55 1 0 1: 39 56 1 6 1: 56 57 1 0 1: 56 58 1 0 1: 38 59 1 0 1: 35 60 1 6 1: 60 61 1 0 1: 61 62 1 0 1: 61 63 1 0 1: 34 64 1 0 1: 31 65 1 6 1: 65 66 1 0 1: 66 67 1 0 1: 66 68 1 0 1: 30 69 1 0 1: 27 70 1 6 1: 23 71 1 6 1: 19 72 1 6 1: 72 73 1 0 1: 73 74 1 0 1: 73 75 1 0 1: 18 76 1 0 1: 15 77 1 6 1: 77 78 1 0 1: 77 79 1 0 1: 11 80 1 6 1: 80 81 1 0 1: 81 82 1 0 1: 81 83 1 0 1: 10 84 1 0 1: 6 85 1 0 1: 46 3 1 0 1: M END 1: 1: single-double 1: RDKit 2D 1: 1: 17 16 0 0 0 0 0 0 0 0999 V2000 1: -6.9282 -0.2298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -6.0618 0.2696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -5.1962 -0.2312 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -4.3298 0.2682 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -3.4642 -0.2326 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.5978 0.2668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.7322 -0.2340 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.8658 0.2654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.0002 -0.2352 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.8662 0.2640 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.7318 -0.2366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.5982 0.2626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.4638 -0.2380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 4.3302 0.2612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 5.1958 -0.2394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 6.0622 0.2598 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: 6.9278 -0.2408 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 2 3 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 9 10 1 0 1: 10 11 2 3 1: 11 12 1 0 1: 12 13 2 3 1: 13 14 1 0 1: 14 15 2 3 1: 15 16 1 0 1: 16 17 1 0 1: M END 1: 1: cis-trans 1: RDKit 2D 1: 1: 10 9 0 0 0 0 0 0 0 0999 V2000 1: -3.6370 -0.2028 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1: -2.7706 -0.7022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.9050 -0.2016 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.0386 -0.7008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1730 -0.2002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.6934 -0.6994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5590 -0.1988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.5582 0.8012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 2.4238 1.3020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 3.2902 0.8026 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 2 0 1: 3 4 1 0 1: 4 5 2 0 1: 5 6 1 0 1: 6 7 2 0 1: 7 8 1 0 1: 8 9 2 0 1: 9 10 1 0 1: M END 1: 1: admntn 1: RDKit 2D 1: 1: 10 12 0 0 0 0 0 0 0 0999 V2000 1: 1.3505 -0.5360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.5267 -1.1020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4629 -1.0366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.7523 0.0052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -1.4741 0.5660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.4761 0.5032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.3505 1.0730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1.0611 0.5080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 0.0643 0.5686 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: -0.1877 -0.5490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1: 1 2 1 0 1: 2 3 1 0 1: 3 4 1 0 1: 4 5 1 0 1: 5 6 1 0 1: 6 7 1 0 1: 7 8 1 0 1: 8 9 1 0 1: 6 10 1 0 1: 8 1 1 0 1: 9 4 1 0 1: 10 2 1 0 1: M END 1: 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) 22: ---------------------------------------------------------------------- 22: Traceback (most recent call last): 22: File "/build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py", line 41, in test1Basic 22: refPts = np.zeros((2, 3), np.float) 22: ^^^^^^^^ 22: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ 22: raise AttributeError(__former_attrs__[attr]) 22: AttributeError: module 'numpy' has no attribute 'float'. 22: `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. 22: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 22: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 22: 22: ====================================================================== 22: ERROR: test2Weights (__main__.TestCase.test2Weights) 22: ---------------------------------------------------------------------- 22: Traceback (most recent call last): 22: File "/build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py", line 79, in test2Weights 22: np.float) 22: ^^^^^^^^ 22: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ 22: raise AttributeError(__former_attrs__[attr]) 22: AttributeError: module 'numpy' has no attribute 'float'. 22: `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. 22: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 22: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 22: 22: ====================================================================== 22: ERROR: test3tetra (__main__.TestCase.test3tetra) 22: ---------------------------------------------------------------------- 22: Traceback (most recent call last): 22: File "/build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py", line 109, in test3tetra 22: np.float) 22: ^^^^^^^^ 22: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ 22: raise AttributeError(__former_attrs__[attr]) 22: AttributeError: module 'numpy' has no attribute 'float'. 22: `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. 22: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 22: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 22: 22: ---------------------------------------------------------------------- 22: Ran 5 tests in 0.003s 22: 22: FAILED (errors=3) 22: Testing Alignment Wrapper code: 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) 28: ---------------------------------------------------------------------- 28: Traceback (most recent call last): 28: File "/build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap/rough_test.py", line 28, in test1SmoothPass 28: arr = np.array([[0, 1.0, 5.0], [1.0, 0, 1.0], [0.0, 1.0, 0]], np.float) 28: ^^^^^^^^ 28: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ 28: raise AttributeError(__former_attrs__[attr]) 28: AttributeError: module 'numpy' has no attribute 'float'. 28: `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. 28: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 28: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 28: 28: ====================================================================== 28: ERROR: test2SmoothFail (__main__.TestCase.test2SmoothFail) 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 28: arr = np.array([[0, 1.0, 5.0], [1.0, 0, 1.0], [3.0, 1.0, 0]], np.float) 28: ^^^^^^^^ 28: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ 28: raise AttributeError(__former_attrs__[attr]) 28: AttributeError: module 'numpy' has no attribute 'float'. 28: `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. 28: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 28: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 28: 28: ====================================================================== 28: ERROR: test3SmoothPass (__main__.TestCase.test3SmoothPass) 28: ---------------------------------------------------------------------- 28: Traceback (most recent call last): 28: File "/build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap/rough_test.py", line 41, in test3SmoothPass 28: arr = np.array([[0, 1.1, 5.0], [0.9, 0, 1.1], [0.0, 0.9, 0]], np.float) 28: ^^^^^^^^ 28: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ 28: raise AttributeError(__former_attrs__[attr]) 28: AttributeError: module 'numpy' has no attribute 'float'. 28: `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. 28: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 28: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 28: 28: ====================================================================== 28: ERROR: test4Embed (__main__.TestCase.test4Embed) 28: ---------------------------------------------------------------------- 28: Traceback (most recent call last): 28: File "/build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap/rough_test.py", line 50, in test4Embed 28: arr = np.array([[0, 1.0, 5.0], [1.0, 0, 1.0], [0.0, 1.0, 0]], np.float) 28: ^^^^^^^^ 28: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ 28: raise AttributeError(__former_attrs__[attr]) 28: AttributeError: module 'numpy' has no attribute 'float'. 28: `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. 28: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 28: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 28: 28: ====================================================================== 28: ERROR: test5EmbedFail (__main__.TestCase.test5EmbedFail) 28: ---------------------------------------------------------------------- 28: Traceback (most recent call last): 28: File "/build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap/rough_test.py", line 61, in test5EmbedFail 28: arr = np.array([[0, 1.0, 5.0], [1.0, 0, 1.0], [3.0, 1.0, 0]], np.float) 28: ^^^^^^^^ 28: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ 28: raise AttributeError(__former_attrs__[attr]) 28: AttributeError: module 'numpy' has no attribute 'float'. 28: `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. 28: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 28: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 28: 28: ====================================================================== 28: ERROR: test6EmbedConstraints (__main__.TestCase.test6EmbedConstraints) 28: ---------------------------------------------------------------------- 28: Traceback (most recent call last): 28: File "/build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap/rough_test.py", line 67, in test6EmbedConstraints 28: arr = np.array([[0.0, 1.0, 1.0], [1.0, 0.0, 1.0], [0.99, 1.0, 0.0]], np.float) 28: ^^^^^^^^ 28: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ 28: raise AttributeError(__former_attrs__[attr]) 28: AttributeError: module 'numpy' has no attribute 'float'. 28: `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. 28: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 28: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 28: 28: ---------------------------------------------------------------------- 28: Ran 6 tests in 0.003s 28: 28: FAILED (errors=6) 22/208 Test #28: pyDistGeom .............................***Failed 0.22 sec EEEEEE ====================================================================== ERROR: test1SmoothPass (__main__.TestCase.test1SmoothPass) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap/rough_test.py", line 28, in test1SmoothPass arr = np.array([[0, 1.0, 5.0], [1.0, 0, 1.0], [0.0, 1.0, 0]], 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: test2SmoothFail (__main__.TestCase.test2SmoothFail) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap/rough_test.py", line 37, in test2SmoothFail arr = np.array([[0, 1.0, 5.0], [1.0, 0, 1.0], [3.0, 1.0, 0]], 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: test3SmoothPass (__main__.TestCase.test3SmoothPass) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap/rough_test.py", line 41, in test3SmoothPass arr = np.array([[0, 1.1, 5.0], [0.9, 0, 1.1], [0.0, 0.9, 0]], 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: test4Embed (__main__.TestCase.test4Embed) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap/rough_test.py", line 50, in test4Embed arr = np.array([[0, 1.0, 5.0], [1.0, 0, 1.0], [0.0, 1.0, 0]], 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: test5EmbedFail (__main__.TestCase.test5EmbedFail) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap/rough_test.py", line 61, in test5EmbedFail arr = np.array([[0, 1.0, 5.0], [1.0, 0, 1.0], [3.0, 1.0, 0]], 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: test6EmbedConstraints (__main__.TestCase.test6EmbedConstraints) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap/rough_test.py", line 67, in test6EmbedConstraints arr = np.array([[0.0, 1.0, 1.0], [1.0, 0.0, 1.0], [0.99, 1.0, 0.0]], 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 6 tests in 0.003s FAILED (errors=6) 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 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 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 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 32: done 32: starting ring finding 32: done 32: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 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 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 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: -------------------------------------------------- 27/208 Test #33: graphmoltestChirality .................. Passed 0.10 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 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 34: 2 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 34: 3 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 34: 4 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 34: 5 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 4 arom?: 0 chi: 0 34: 6 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 34: Bonds: 34: 0 0->1 order: 1 conj?: 0 aromatic?: 0 34: 1 1->2 order: 1 conj?: 0 aromatic?: 0 34: 2 2->0 order: 1 conj?: 0 aromatic?: 0 34: 3 3->4 order: 1 conj?: 0 aromatic?: 0 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: [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: [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 34: smi match: *OS(=O)OC *OS(=O)OC 34: smi match: *S(=O)(=O)OC *S(=O)(=O)OC 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 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 34: smi match: OS(=O)(=O)C(F)(F)F OS(=O)(=O)C(F)(F)F 34: smi match: SP(S)=S SP(S)=S 34: smi match: NP(N)(N)=O NP(N)(N)=O 34: smi match: cN=[N+]=[N-] cN=[N+]=[N-] 34: smi match: *CC=O *CC=O 34: smi match: NNC=O NNC=O 34: smi match: * * 34: smi match: C=P C=P 34: smi match: CC(=N)Cl CC(=N)Cl 34: smi match: N=O N=O 34: smi match: ** ** 34: smi match: N=C=N N=C=N 34: smi match: [C-]#[NH+] [C-]#[NH+] 34: smi match: O=CON(C=O)C=O O=CON(C=O)C=O 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 34: smi match: CCOP(=O)(C#N)OCC CCOP(=O)(C#N)OCC 34: smi match: N#CN=N N#CN=N 34: smi match: N=NCC=O N=NCC=O 34: smi match: CCCCCCC CCCCCCC 34: smi match: OCCOCCO OCCOCCO 34: smi match: SS SS 34: smi match: [SH] [SH] 34: smi match: *1CC1 *1CC1 34: smi match: [OH]ccc([OH])c[OH] [OH]ccc([OH])c[OH] 34: smi match: [OH]cc([OH])c[OH] [OH]cc([OH])c[OH] 34: smi match: NC(=S)N=N NC(=S)N=N 34: smi match: N#CS N#CS 34: smi match: cC[N+] cC[N+] 34: smi match: C*C=S C*C=S 34: smi match: N[CH2]C#N N[CH2]C#N 34: smi match: O=C1CCO1 O=C1CCO1 34: smi match: O=P([OH])OP(=O)[OH] O=P([OH])OP(=O)[OH] 34: smi match: O=C1CCN1 O=C1CCN1 34: smi match: O=C1C~CC(=O)C~C1 O=C1C~CC(=O)C~C1 34: smi match: C=CC=CC=CC=C C=CC=CC=CC=C 34: smi match: C1CCC(OC2CCC3CCCCC3C2)OC1 C1CCC(OC2CCC3CCCCC3C2)OC1 34: smi match: O=C1NCC2CCCCC21 O=C1NCC2CCCCC21 34: smi match: O=C1CCCC(=O)N1 O=C1CCCC(=O)N1 34: smi match: C1CCC(C2CCCO2)OC1 C1CCC(C2CCCO2)OC1 34: smi match: [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 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 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 34: smi match: * * 34: smi match: * * 34: smi match: *C=C *C=C 34: smi match: N#CS N#CS 34: smi match: *C=S *C=S 34: smi match: *N *N 34: smi match: *C(=C)C=O *C(=C)C=O 34: smi match: *C#C *C#C 34: smi match: N#CCO N#CCO 34: smi match: O=N(=O)CCO O=N(=O)CCO 34: smi match: N=CS N=CS 34: smi match: O=CNC(O)C=O O=CNC(O)C=O 34: smi match: C=C(C=O)C=O C=C(C=O)C=O 34: smi match: N=CC=O N=CC=O 34: smi match: *C(C=O)C=O *C(C=O)C=O 34: smi match: *C(C=O)=C(*)C=O *C(C=O)=C(*)C=O 34: smi match: O=CC=CC=O O=CC=CC=O 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 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 34: smi match: O=CS O=CS 34: smi match: O=CSC=S O=CSC=S 34: smi match: S=CS S=CS 34: smi match: C=O C=O 34: smi match: *C=N *C=N 34: smi match: CCCCCCC CCCCCCC 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 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 34: smi match: C=CC=O C=CC=O 34: smi match: C=CC(=O)C=C C=CC(=O)C=C 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 34: smi match: C=CC=N C=CC=N 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 34: smi match: C=CO C=CO 34: smi match: C=COC=O C=COC=O 34: smi match: C=CS C=CS 34: smi match: C=C[SH](=O)=O C=C[SH](=O)=O 34: smi match: C=NCO C=NCO 34: smi match: C=NC=O C=NC=O 34: smi match: C=NN C=NN 34: smi match: C=NN=C C=NN=C 34: smi match: C=NO C=NO 34: smi match: C=NOC=O C=NOC=O 34: smi match: C=N=O C=N=O 34: smi match: N#CS N#CS 34: smi match: *CN=O *CN=O 34: smi match: NCN NCN 34: smi match: ON=CCN=O ON=CCN=O 34: smi match: NC(S)=N[SH](=O)=O NC(S)=N[SH](=O)=O 34: smi match: N=C(N)S N=C(N)S 34: smi match: NC(=O)Oc1ccccc1 NC(=O)Oc1ccccc1 34: smi match: NC=S NC=S 34: smi match: NC(N)=S NC(N)=S 34: smi match: C=CN C=CN 34: smi match: NOC=O NOC=O 34: smi match: C1CN1 C1CN1 34: smi match: O=C1NNNN1 O=C1NNNN1 34: smi match: N=C(N)C(=N)N N=C(N)C(=N)N 34: smi match: N=C(N)O N=C(N)O 34: smi match: N=C(N)C(=N)S N=C(N)C(=N)S 34: smi match: *C=N *C=N 34: smi match: N=CC=O N=CC=O 34: smi match: N=CS N=CS 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 34: smi match: NOC(=O)O NOC(=O)O 34: smi match: *C(O)=S *C(O)=S 34: smi match: C=CO C=CO 34: smi match: ON=CC=NO ON=CC=NO 34: smi match: *C[SH](=O)=O *C[SH](=O)=O 34: smi match: OS(=O)=O OS(=O)=O 34: smi match: N#CS N#CS 34: smi match: C=C(S)S C=C(S)S 34: smi match: N=C(N)S N=C(N)S 34: smi match: N=C(S)S N=C(S)S 34: smi match: NC(=S)S NC(=S)S 34: smi match: O=CNS O=CNS 34: smi match: S S 34: smi match: [SiH4] [SiH4] 34: smi match: NS NS 34: smi match: NCN NCN 34: smi match: cC(c)(O)O cC(c)(O)O 34: smi match: *C(c)O *C(c)O 34: smi match: C=CS(c)(=O)=O C=CS(c)(=O)=O 34: smi match: cS(=O)(=O)O cS(=O)(=O)O 34: smi match: *c1ccccn1=O *c1ccccn1=O 34: smi match: *c1ccccn1 *c1ccccn1 34: smi match: *c1nccccn1 *c1nccccn1 34: smi match: C1COCOC1 C1COCOC1 34: smi match: C=S C=S 34: smi match: c=S c=S 34: smi match: S=CS S=CS 34: smi match: C=CN(=O)=O C=CN(=O)=O 34: smi match: C=CN(=O)O C=CN(=O)O 34: smi match: N=CC=O N=CC=O 34: smi match: C=CS C=CS 34: smi match: SC(S)(S)S SC(S)(S)S 34: smi match: OS(O)(O)O OS(O)(O)O 34: smi match: O=N(=O)C[SH](=O)=O O=N(=O)C[SH](=O)=O 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 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 34: smi match: N=C(=N)S N=C(=N)S 34: smi match: O=N=O O=N=O 34: smi match: O=NO O=NO 34: smi match: ONO ONO 34: smi match: C1SCS1 C1SCS1 34: smi match: N=C=S N=C=S 34: smi match: N=C=N N=C=N 34: smi match: C1N=N1 C1N=N1 34: smi match: *CS *CS 34: smi match: SC(S)=C(S)S SC(S)=C(S)S 34: smi match: N=CC=NO N=CC=NO 34: smi match: N#CCC#N N#CCC#N 34: smi match: CON=O CON=O 34: smi match: C=CN C=CN 34: smi match: C=N[SH](=O)=O C=N[SH](=O)=O 34: smi match: NN=O NN=O 34: smi match: NC(=O)S NC(=O)S 34: smi match: N#CS N#CS 34: smi match: NC(=O)C(N)=O NC(=O)C(N)=O 34: smi match: c=N c=N 34: smi match: C1COCO1 C1COCO1 34: smi match: C=NN[SH](=O)=O C=NN[SH](=O)=O 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 34: smi match: ONO ONO 34: smi match: ON(~O)~O ON(~O)~O 34: smi match: OC1COC(O)C1 OC1COC(O)C1 34: smi match: OC1CCOC1O OC1CCOC1O 34: smi match: OC1CCOC(O)C1 OC1CCOC(O)C1 34: smi match: N=[N+]=N N=[N+]=N 34: smi match: N#CN N#CN 34: smi match: C=NN=C C=NN=C 34: smi match: *CCN(C)C *CCN(C)C 34: smi match: CNN CNN 34: smi match: *CC *CC 34: smi match: OCS OCS 34: smi match: C1NO1 C1NO1 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 34: smi match: *C(*)=C *C(*)=C 34: smi match: N#[NH+] N#[NH+] 34: smi match: C#NO C#NO 34: smi match: OOO OOO 34: smi match: OO OO 34: smi match: O~Cl(~O)~O O~Cl(~O)~O 34: smi match: O~Cl(~O)(~O)~O O~Cl(~O)(~O)~O 34: smi match: [OH]~C(~O)~O [OH]~C(~O)~O 34: smi match: *N *N 34: smi match: *P *P 34: smi match: *S *S 34: smi match: *C(*)(*)C=C *C(*)(*)C=C 34: smi match: *C(*)(*)C=C *C(*)(*)C=C 34: smi match: *C(*)C=C *C(*)C=C 34: smi match: *CC=C *CC=C 34: smi match: CN=C=O CN=C=O 34: smi match: CN=C=S CN=C=S 34: smi match: *C=O *C=O 34: smi match: N=N N=N 34: smi match: SS SS 34: smi match: O=C1CCNC(=O)O1 O=C1CCNC(=O)O1 34: smi match: CSC(C)=N CSC(C)=N 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 34: smi match: C=CC#N C=CC#N 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 34: smi match: C#CC#N C#CC#N 34: smi match: C#CC=O C#CC=O 34: smi match: C#CC(=O)OCC C#CC(=O)OCC 34: smi match: C#CC=O C#CC=O 34: smi match: *C(=O)C#C *C(=O)C#C 34: smi match: C=CC=O C=CC=O 34: smi match: *C(*)(*)O *C(*)(*)O 34: smi match: COS(O)(=O)=O COS(O)(=O)=O 34: smi match: CS(=O)(=O)[O-] CS(=O)(=O)[O-] 34: smi match: NS(=O)(=O)[O-] NS(=O)(=O)[O-] 34: smi match: *C(*)(*)C=O *C(*)(*)C=O 34: smi match: *C(*)(*)C=O *C(*)(*)C=O 34: smi match: *C(*)C=O *C(*)C=O 34: smi match: *CC=O *CC=O 34: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O 34: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O 34: smi match: *C(*)[SH](=O)=O *C(*)[SH](=O)=O 34: smi match: *C[SH](=O)=O *C[SH](=O)=O 34: smi match: * * 34: smi match: *1CC1 *1CC1 34: smi match: O=COC=O O=COC=O 34: smi match: N=C=O N=C=O 34: smi match: N=C=S N=C=S 34: smi match: O~O O~O 34: smi match: N~[SiH4] N~[SiH4] 34: smi match: *P *P 34: smi match: C=N=N C=N=N 34: smi match: *N#[NH+] *N#[NH+] 34: smi match: *S* *S* 34: smi match: ** ** 34: smi match: *CC* *CC* 34: smi match: *O[SiH3] *O[SiH3] 34: smi match: *OS(*)~O *OS(*)~O 34: smi match: N~N~O N~N~O 34: smi match: *N(~O)(~O)~O *N(~O)(~O)~O 34: smi match: *[N+](=C)[O-] *[N+](=C)[O-] 34: smi match: * * 34: smi match: *C(*)NCN(*)* *C(*)NCN(*)* 34: smi match: *OCC#N *OCC#N 34: smi match: **C=C **C=C 34: smi match: C=C[O-] C=C[O-] 34: smi match: C=CO C=CO 34: smi match: * * 34: smi match: O=CON1C(=O)CCC1=O O=CON1C(=O)CCC1=O 34: smi match: O=COn1ccnc1 O=COn1ccnc1 34: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F 34: smi match: CC(C)(C)S CC(C)(C)S 34: smi match: [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C 34: smi match: [CH]=O [CH]=O 34: smi match: C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C 34: smi match: SS SS 34: smi match: [SH] [SH] 34: smi match: *C* *C* 34: smi match: * * 34: smi match: C[nH3+] C[nH3+] 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* 34: smi match: * * 34: smi match: * * 34: smi match: * * 34: smi match: *N=C(*)* *N=C(*)* 34: smi match: *C(*)(*)C=O *C(*)(*)C=O 34: smi match: CSC=O CSC=O 34: smi match: * * 34: smi match: O=CCl O=CCl 34: smi match: *** *** 34: smi match: *C=O *C=O 34: smi match: C[OH] C[OH] 34: smi match: C[OH] C[OH] 34: smi match: C[OH] C[OH] 34: smi match: C[OH] C[OH] 34: smi match: C[CH]=O C[CH]=O 34: smi match: *=* *=* 34: smi match: *C *C 34: smi match: C#C C#C 34: smi match: *[CH]C=C *[CH]C=C 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] 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 34: smi match: *N(*)C*=O *N(*)C*=O 34: smi match: O=*C[OH] O=*C[OH] 34: smi match: *=C*=O *=C*=O 34: smi match: *=CC#N *=CC#N 34: smi match: *C[OH] *C[OH] 34: smi match: ** ** 34: smi match: *C[OH] *C[OH] 34: smi match: *C(*)=O *C(*)=O 34: smi match: * * 34: smi match: *CC(=O)[OH] *CC(=O)[OH] 34: smi match: CC(=O)OC(C)=O CC(=O)OC(C)=O 34: smi match: *c *c 34: smi match: CN(C)c CN(C)c 34: smi match: c c 34: smi match: *c *c 34: smi match: *c *c 34: smi match: **:*cF **:*cF 34: smi match: cB([OH])[OH] cB([OH])[OH] 34: smi match: N~N~N N~N~N 34: smi match: *N=N* *N=N* 34: smi match: *CC[OH] *CC[OH] 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] 34: smi match: *OC(=O)O* *OC(=O)O* 34: smi match: * * 34: smi match: *OC(=O)Cl *OC(=O)Cl 34: smi match: *C#N *C#N 34: smi match: NCC(=O)NCC=O NCC(=O)NCC=O 34: smi match: SS SS 34: smi match: * * 34: smi match: *=* *=* 34: smi match: *=* *=* 34: smi match: *=* *=* 34: smi match: *=* *=* 34: smi match: C1CO1 C1CO1 34: smi match: *OC(*)=O *OC(*)=O 34: smi match: * * 34: smi match: *O*[OH] *O*[OH] 34: smi match: COC(C)(C)O COC(C)(C)O 34: smi match: *[OH] *[OH] 34: smi match: ** ** 34: smi match: C=N[NH2] C=N[NH2] 34: smi match: C=NC=O C=NC=O 34: smi match: * * 34: smi match: C#NC C#NC 34: smi match: CN=C=O CN=C=O 34: smi match: CN=C=S CN=C=S 34: smi match: *OC(*)(*)O* *OC(*)(*)O* 34: smi match: *C(*)=O *C(*)=O 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 34: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH] 34: smi match: * * 34: smi match: *C#N *C#N 34: smi match: *N(=O)~O *N(=O)~O 34: smi match: N N 34: smi match: OC(=O)C(O)=O OC(=O)C(O)=O 34: smi match: C=NO C=NO 34: smi match: O~O O~O 34: smi match: c[OH] c[OH] 34: smi match: O=P(~[OH])~O O=P(~[OH])~O 34: smi match: CO~P(=O)~O CO~P(=O)~O 34: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O 34: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O 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: * * 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 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 34: smi match: *S(C)(~O)~O *S(C)(~O)~O 34: smi match: CN(C)C CN(C)C 34: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 34: smi match: *C(*)=S *C(*)=S 34: smi match: *OC(*)=S *OC(*)=S 34: smi match: * * 34: smi match: C[SH] C[SH] 34: smi match: c[SH] c[SH] 34: smi match: NC(N)=S NC(N)=S 34: smi match: * * 34: smi match: ***** ***** 34: smi match: NC(N)=O NC(N)=O 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 59: [16:02:58] 59: ----------------------------------------- 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 60: [16:02:59] 60: ----------------------------------------- 60: [16:02:59] Finished: testDetermineFormat() 60: [16:02:59] ----------------------------------------- 60: 60: [16:02:59] 60: ----------------------------------------- 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 60: [16:02:59] Finished: testSdf() 60: [16:02:59] ----------------------------------------- 60: 60: [16:02:59] 60: ----------------------------------------- 61: [16:02:59] 61: ----------------------------------------- 60: [16:02:59] Finished: testSmi() 60: [16:02:59] ----------------------------------------- 60: 60: [16:02:59] 60: ----------------------------------------- 60: [16:02:59] Finished: testMae() 60: [16:02:59] ----------------------------------------- 60: 60: [16:02:59] 60: ----------------------------------------- 60: [16:02:59] Finished: testTdt() 60: [16:02:59] ----------------------------------------- 60: 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 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 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 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 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 65: PDB: 65: ATOM 1 N GLY A 1 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 3 C GLY A 1 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 4 O GLY A 1 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 5 N ARG A 2 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 6 CA ARG A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 7 C ARG A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 8 O ARG A 2 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 9 CB ARG A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 10 CG ARG A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 11 CD ARG A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 12 NE ARG A 2 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 13 CZ ARG A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 14 NH1 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 15 NH2 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 16 N GLU A 3 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 17 CA GLU A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 18 C GLU A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 23 OE1 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 24 OE2 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 25 N GLY A 4 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 26 CA GLY A 4 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 27 C GLY A 4 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 28 O GLY A 4 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 29 OXT GLY A 4 0.000 0.000 0.000 1.00 0.00 O 65: CONECT 1 2 65: CONECT 2 3 65: CONECT 3 4 4 5 65: CONECT 5 6 65: CONECT 6 7 9 65: CONECT 7 8 8 16 65: CONECT 9 10 65: CONECT 10 11 65: CONECT 11 12 65: CONECT 12 13 65: CONECT 13 14 14 15 65: CONECT 16 17 65: CONECT 17 18 20 65: CONECT 18 19 19 25 65: CONECT 20 21 65: CONECT 21 22 65: CONECT 22 23 23 24 65: CONECT 25 26 65: CONECT 26 27 65: CONECT 27 28 28 29 65: END 65: 65: Sequence: TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN 65: HELM: PEPTIDE1{T.T.C.C.P.S.I.V.A.R.S.N.F.N.V.C.R.L.P.G.T.P.E.A.I.C.A.T.Y.T.G.C.I.I.I.P.G.A.T.C.P.G.D.Y.A.N}$$$$ 65: Smiles: CC[C@H](C)[C@H](NC(=O)[C@H](C)NC(=O)[C@H](CCC(=O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H](NC(=O)CNC(=O)[C@@H]1CCCN1C(=O)[C@H](CC(C)C)NC(=O)[C@H](CCCNC(=N)N)NC(=O)[C@H](CS)NC(=O)[C@@H](NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](CO)NC(=O)[C@H](CCCNC(=N)N)NC(=O)[C@H](C)NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H](CO)NC(=O)[C@@H]1CCCN1C(=O)[C@H](CS)NC(=O)[C@H](CS)NC(=O)[C@@H](NC(=O)[C@@H](N)[C@@H](C)O)[C@@H](C)O)[C@@H](C)CC)C(C)C)C(C)C)[C@@H](C)O)C(=O)N[C@@H](CS)C(=O)N[C@@H](C)C(=O)N[C@H](C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@H](C(=O)NCC(=O)N[C@@H](CS)C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N1CCC[C@H]1C(=O)NCC(=O)N[C@@H](C)C(=O)N[C@H](C(=O)N[C@@H](CS)C(=O)N1CCC[C@H]1C(=O)NCC(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@@H](C)C(=O)N[C@@H](CC(N)=O)C(=O)O)[C@@H](C)O)[C@@H](C)CC)[C@@H](C)CC)[C@@H](C)CC)[C@@H](C)O)[C@@H](C)O 65: PDB: 65: ATOM 1 N THR A 1 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 2 CA THR A 1 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 3 C THR A 1 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 4 O THR A 1 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 5 CB THR A 1 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 6 OG1 THR A 1 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 7 CG2 THR A 1 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 8 N THR A 2 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 9 CA THR A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 10 C THR A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 11 O THR A 2 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 12 CB THR A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 13 OG1 THR A 2 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 14 CG2 THR A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 15 N CYS A 3 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 16 CA CYS A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 17 C CYS A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 18 O CYS A 3 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 19 CB CYS A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 20 SG CYS A 3 0.000 0.000 0.000 1.00 0.00 S 65: ATOM 21 N CYS A 4 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 22 CA CYS A 4 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 23 C CYS A 4 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 24 O CYS A 4 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 25 CB CYS A 4 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 26 SG CYS A 4 0.000 0.000 0.000 1.00 0.00 S 65: ATOM 27 N PRO A 5 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 28 CA PRO A 5 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 29 C PRO A 5 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 30 O PRO A 5 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 31 CB PRO A 5 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 32 CG PRO A 5 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 33 CD PRO A 5 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 34 N SER A 6 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 35 CA SER A 6 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 36 C SER A 6 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 37 O SER A 6 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 38 CB SER A 6 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 39 OG SER A 6 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 40 N ILE A 7 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 41 CA ILE A 7 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 42 C ILE A 7 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 43 O ILE A 7 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 44 CB ILE A 7 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 45 CG1 ILE A 7 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 46 CG2 ILE A 7 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 47 CD1 ILE A 7 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 48 N VAL A 8 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 49 CA VAL A 8 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 50 C VAL A 8 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 51 O VAL A 8 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 52 CB VAL A 8 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 53 CG1 VAL A 8 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 54 CG2 VAL A 8 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 55 N ALA A 9 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 56 CA ALA A 9 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 57 C ALA A 9 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 58 O ALA A 9 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 59 CB ALA A 9 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 60 N ARG A 10 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 61 CA ARG A 10 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 62 C ARG A 10 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 63 O ARG A 10 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 64 CB ARG A 10 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 65 CG ARG A 10 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 66 CD ARG A 10 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 67 NE ARG A 10 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 68 CZ ARG A 10 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 69 NH1 ARG A 10 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 70 NH2 ARG A 10 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 71 N SER A 11 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 72 CA SER A 11 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 73 C SER A 11 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 74 O SER A 11 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 75 CB SER A 11 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 76 OG SER A 11 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 77 N ASN A 12 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 78 CA ASN A 12 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 79 C ASN A 12 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 80 O ASN A 12 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 81 CB ASN A 12 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 82 CG ASN A 12 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 83 OD1 ASN A 12 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 84 ND2 ASN A 12 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 85 N PHE A 13 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 86 CA PHE A 13 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 87 C PHE A 13 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 88 O PHE A 13 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 89 CB PHE A 13 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 90 CG PHE A 13 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 91 CD1 PHE A 13 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 92 CD2 PHE A 13 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 93 CE1 PHE A 13 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 94 CE2 PHE A 13 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 95 CZ PHE A 13 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 96 N ASN A 14 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 97 CA ASN A 14 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 98 C ASN A 14 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 99 O ASN A 14 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 100 CB ASN A 14 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 101 CG ASN A 14 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 102 OD1 ASN A 14 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 103 ND2 ASN A 14 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 104 N VAL A 15 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 105 CA VAL A 15 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 106 C VAL A 15 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 107 O VAL A 15 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 108 CB VAL A 15 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 109 CG1 VAL A 15 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 110 CG2 VAL A 15 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 111 N CYS A 16 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 112 CA CYS A 16 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 113 C CYS A 16 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 114 O CYS A 16 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 115 CB CYS A 16 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 116 SG CYS A 16 0.000 0.000 0.000 1.00 0.00 S 65: ATOM 117 N ARG A 17 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 118 CA ARG A 17 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 119 C ARG A 17 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 120 O ARG A 17 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 121 CB ARG A 17 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 122 CG ARG A 17 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 123 CD ARG A 17 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 124 NE ARG A 17 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 125 CZ ARG A 17 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 126 NH1 ARG A 17 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 127 NH2 ARG A 17 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 128 N LEU A 18 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 129 CA LEU A 18 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 130 C LEU A 18 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 131 O LEU A 18 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 132 CB LEU A 18 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 133 CG LEU A 18 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 134 CD1 LEU A 18 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 135 CD2 LEU A 18 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 136 N PRO A 19 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 137 CA PRO A 19 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 138 C PRO A 19 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 139 O PRO A 19 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 140 CB PRO A 19 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 141 CG PRO A 19 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 142 CD PRO A 19 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 143 N GLY A 20 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 144 CA GLY A 20 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 145 C GLY A 20 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 146 O GLY A 20 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 147 N THR A 21 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 148 CA THR A 21 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 149 C THR A 21 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 150 O THR A 21 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 151 CB THR A 21 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 152 OG1 THR A 21 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 153 CG2 THR A 21 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 154 N PRO A 22 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 155 CA PRO A 22 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 156 C PRO A 22 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 157 O PRO A 22 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 158 CB PRO A 22 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 159 CG PRO A 22 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 160 CD PRO A 22 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 161 N GLU A 23 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 162 CA GLU A 23 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 163 C GLU A 23 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 164 O GLU A 23 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 165 CB GLU A 23 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 166 CG GLU A 23 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 167 CD GLU A 23 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 168 OE1 GLU A 23 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 169 OE2 GLU A 23 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 170 N ALA A 24 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 171 CA ALA A 24 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 172 C ALA A 24 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 173 O ALA A 24 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 174 CB ALA A 24 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 175 N ILE A 25 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 176 CA ILE A 25 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 177 C ILE A 25 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 178 O ILE A 25 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 179 CB ILE A 25 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 180 CG1 ILE A 25 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 181 CG2 ILE A 25 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 182 CD1 ILE A 25 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 183 N CYS A 26 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 184 CA CYS A 26 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 185 C CYS A 26 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 186 O CYS A 26 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 187 CB CYS A 26 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 188 SG CYS A 26 0.000 0.000 0.000 1.00 0.00 S 65: ATOM 189 N ALA A 27 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 190 CA ALA A 27 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 191 C ALA A 27 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 192 O ALA A 27 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 193 CB ALA A 27 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 194 N THR A 28 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 195 CA THR A 28 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 196 C THR A 28 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 197 O THR A 28 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 198 CB THR A 28 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 199 OG1 THR A 28 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 200 CG2 THR A 28 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 201 N TYR A 29 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 202 CA TYR A 29 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 203 C TYR A 29 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 204 O TYR A 29 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 205 CB TYR A 29 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 206 CG TYR A 29 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 207 CD1 TYR A 29 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 208 CD2 TYR A 29 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 209 CE1 TYR A 29 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 210 CE2 TYR A 29 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 211 CZ TYR A 29 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 212 OH TYR A 29 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 213 N THR A 30 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 214 CA THR A 30 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 215 C THR A 30 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 216 O THR A 30 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 217 CB THR A 30 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 218 OG1 THR A 30 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 219 CG2 THR A 30 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 220 N GLY A 31 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 221 CA GLY A 31 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 222 C GLY A 31 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 223 O GLY A 31 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 224 N CYS A 32 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 225 CA CYS A 32 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 226 C CYS A 32 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 227 O CYS A 32 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 228 CB CYS A 32 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 229 SG CYS A 32 0.000 0.000 0.000 1.00 0.00 S 65: ATOM 230 N ILE A 33 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 231 CA ILE A 33 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 232 C ILE A 33 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 233 O ILE A 33 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 234 CB ILE A 33 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 235 CG1 ILE A 33 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 236 CG2 ILE A 33 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 237 CD1 ILE A 33 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 238 N ILE A 34 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 239 CA ILE A 34 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 240 C ILE A 34 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 241 O ILE A 34 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 242 CB ILE A 34 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 243 CG1 ILE A 34 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 244 CG2 ILE A 34 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 245 CD1 ILE A 34 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 246 N ILE A 35 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 247 CA ILE A 35 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 248 C ILE A 35 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 249 O ILE A 35 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 250 CB ILE A 35 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 251 CG1 ILE A 35 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 252 CG2 ILE A 35 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 253 CD1 ILE A 35 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 254 N PRO A 36 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 255 CA PRO A 36 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 256 C PRO A 36 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 257 O PRO A 36 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 258 CB PRO A 36 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 259 CG PRO A 36 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 260 CD PRO A 36 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 261 N GLY A 37 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 262 CA GLY A 37 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 263 C GLY A 37 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 264 O GLY A 37 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 265 N ALA A 38 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 266 CA ALA A 38 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 267 C ALA A 38 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 268 O ALA A 38 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 269 CB ALA A 38 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 270 N THR A 39 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 271 CA THR A 39 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 272 C THR A 39 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 273 O THR A 39 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 274 CB THR A 39 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 275 OG1 THR A 39 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 276 CG2 THR A 39 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 277 N CYS A 40 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 278 CA CYS A 40 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 279 C CYS A 40 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 280 O CYS A 40 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 281 CB CYS A 40 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 282 SG CYS A 40 0.000 0.000 0.000 1.00 0.00 S 65: ATOM 283 N PRO A 41 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 284 CA PRO A 41 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 285 C PRO A 41 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 286 O PRO A 41 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 287 CB PRO A 41 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 288 CG PRO A 41 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 289 CD PRO A 41 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 290 N GLY A 42 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 291 CA GLY A 42 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 292 C GLY A 42 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 293 O GLY A 42 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 294 N ASP A 43 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 295 CA ASP A 43 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 296 C ASP A 43 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 297 O ASP A 43 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 298 CB ASP A 43 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 299 CG ASP A 43 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 300 OD1 ASP A 43 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 301 OD2 ASP A 43 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 302 N TYR A 44 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 303 CA TYR A 44 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 304 C TYR A 44 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 305 O TYR A 44 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 306 CB TYR A 44 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 307 CG TYR A 44 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 308 CD1 TYR A 44 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 309 CD2 TYR A 44 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 310 CE1 TYR A 44 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 311 CE2 TYR A 44 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 312 CZ TYR A 44 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 313 OH TYR A 44 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 314 N ALA A 45 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 315 CA ALA A 45 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 316 C ALA A 45 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 317 O ALA A 45 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 318 CB ALA A 45 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 319 N ASN A 46 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 320 CA ASN A 46 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 321 C ASN A 46 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 322 O ASN A 46 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 323 CB ASN A 46 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 324 CG ASN A 46 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 325 OD1 ASN A 46 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 326 ND2 ASN A 46 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 327 OXT ASN A 46 0.000 0.000 0.000 1.00 0.00 O 65: CONECT 1 2 65: CONECT 2 3 5 65: CONECT 3 4 4 8 65: CONECT 5 6 7 65: CONECT 8 9 65: CONECT 9 10 12 65: CONECT 10 11 11 15 65: CONECT 12 13 14 65: CONECT 15 16 65: CONECT 16 17 19 65: CONECT 17 18 18 21 65: CONECT 19 20 65: CONECT 21 22 65: CONECT 22 23 25 65: CONECT 23 24 24 27 65: CONECT 25 26 65: CONECT 27 28 33 65: CONECT 28 29 31 65: CONECT 29 30 30 34 65: CONECT 31 32 65: CONECT 32 33 65: CONECT 34 35 65: CONECT 35 36 38 65: CONECT 36 37 37 40 65: CONECT 38 39 65: CONECT 40 41 65: CONECT 41 42 44 65: CONECT 42 43 43 48 65: CONECT 44 45 46 65: CONECT 46 47 65: CONECT 48 49 65: CONECT 49 50 52 65: CONECT 50 51 51 55 65: CONECT 52 53 54 65: CONECT 55 56 65: CONECT 56 57 59 65: CONECT 57 58 58 60 65: CONECT 60 61 65: CONECT 61 62 64 65: CONECT 62 63 63 71 65: CONECT 64 65 65: CONECT 65 66 65: CONECT 66 67 65: CONECT 67 68 65: CONECT 68 69 69 70 65: CONECT 71 72 65: CONECT 72 73 75 65: CONECT 73 74 74 77 65: CONECT 75 76 65: CONECT 77 78 65: CONECT 78 79 81 65: CONECT 79 80 80 85 65: CONECT 81 82 65: CONECT 82 83 83 84 65: CONECT 85 86 65: CONECT 86 87 89 65: CONECT 87 88 88 96 65: CONECT 89 90 65: CONECT 90 91 91 92 65: CONECT 91 93 65: CONECT 92 94 94 65: CONECT 93 95 95 65: CONECT 94 95 65: CONECT 96 97 65: CONECT 97 98 100 65: CONECT 98 99 99 104 65: CONECT 100 101 65: CONECT 101 102 102 103 65: CONECT 104 105 65: CONECT 105 106 108 65: CONECT 106 107 107 111 65: CONECT 108 109 110 65: CONECT 111 112 65: CONECT 112 113 115 65: CONECT 113 114 114 117 65: CONECT 115 116 65: CONECT 117 118 65: CONECT 118 119 121 65: CONECT 119 120 120 128 65: CONECT 121 122 65: CONECT 122 123 65: CONECT 123 124 65: CONECT 124 125 65: CONECT 125 126 126 127 65: CONECT 128 129 65: CONECT 129 130 132 65: CONECT 130 131 131 136 65: CONECT 132 133 65: CONECT 133 134 135 65: CONECT 136 137 142 65: CONECT 137 138 140 65: CONECT 138 139 139 143 65: CONECT 140 141 65: CONECT 141 142 65: CONECT 143 144 65: CONECT 144 145 65: CONECT 145 146 146 147 65: CONECT 147 148 65: CONECT 148 149 151 65: CONECT 149 150 150 154 65: CONECT 151 152 153 65: CONECT 154 155 160 65: CONECT 155 156 158 65: CONECT 156 157 157 161 65: CONECT 158 159 65: CONECT 159 160 65: CONECT 161 162 65: CONECT 162 163 165 65: CONECT 163 164 164 170 65: CONECT 165 166 65: CONECT 166 167 65: CONECT 167 168 168 169 65: CONECT 170 171 65: CONECT 171 172 174 65: CONECT 172 173 173 175 65: CONECT 175 176 65: CONECT 176 177 179 65: CONECT 177 178 178 183 65: CONECT 179 180 181 65: CONECT 181 182 65: CONECT 183 184 65: CONECT 184 185 187 65: CONECT 185 186 186 189 65: CONECT 187 188 65: CONECT 189 190 65: CONECT 190 191 193 65: CONECT 191 192 192 194 65: CONECT 194 195 65: CONECT 195 196 198 65: CONECT 196 197 197 201 65: CONECT 198 199 200 65: CONECT 201 202 65: CONECT 202 203 205 65: CONECT 203 204 204 213 65: CONECT 205 206 65: CONECT 206 207 207 208 65: CONECT 207 209 65: CONECT 208 210 210 65: CONECT 209 211 211 65: CONECT 210 211 65: CONECT 211 212 65: CONECT 213 214 65: CONECT 214 215 217 65: CONECT 215 216 216 220 65: CONECT 217 218 219 65: CONECT 220 221 65: CONECT 221 222 65: CONECT 222 223 223 224 65: CONECT 224 225 65: CONECT 225 226 228 65: CONECT 226 227 227 230 65: CONECT 228 229 65: CONECT 230 231 65: CONECT 231 232 234 65: CONECT 232 233 233 238 65: CONECT 234 235 236 65: CONECT 236 237 65: CONECT 238 239 65: CONECT 239 240 242 65: CONECT 240 241 241 246 65: CONECT 242 243 244 65: CONECT 244 245 65: CONECT 246 247 65: CONECT 247 248 250 65: CONECT 248 249 249 254 65: CONECT 250 251 252 65: CONECT 252 253 65: CONECT 254 255 260 65: CONECT 255 256 258 65: CONECT 256 257 257 261 65: CONECT 258 259 65: CONECT 259 260 65: CONECT 261 262 65: CONECT 262 263 65: CONECT 263 264 264 265 65: CONECT 265 266 65: CONECT 266 267 269 65: CONECT 267 268 268 270 65: CONECT 270 271 65: CONECT 271 272 274 65: CONECT 272 273 273 277 65: CONECT 274 275 276 65: CONECT 277 278 65: CONECT 278 279 281 65: CONECT 279 280 280 283 65: CONECT 281 282 65: CONECT 283 284 289 65: CONECT 284 285 287 65: CONECT 285 286 286 290 65: CONECT 287 288 65: CONECT 288 289 65: CONECT 290 291 65: CONECT 291 292 65: CONECT 292 293 293 294 65: CONECT 294 295 65: CONECT 295 296 298 65: CONECT 296 297 297 302 65: CONECT 298 299 65: CONECT 299 300 300 301 65: CONECT 302 303 65: CONECT 303 304 306 65: CONECT 304 305 305 314 65: CONECT 306 307 65: CONECT 307 308 308 309 65: CONECT 308 310 65: CONECT 309 311 311 65: CONECT 310 312 312 65: CONECT 311 312 65: CONECT 312 313 65: CONECT 314 315 65: CONECT 315 316 318 65: CONECT 316 317 317 319 65: CONECT 319 320 65: CONECT 320 321 323 65: CONECT 321 322 322 327 65: CONECT 323 324 65: CONECT 324 325 325 326 65: END 65: 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 65: PDB: 65: ATOM 1 N GLY A 1 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 3 C GLY A 1 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 4 O GLY A 1 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 5 N ARG A 2 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 6 CA ARG A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 7 C ARG A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 8 O ARG A 2 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 9 CB ARG A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 10 CG ARG A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 11 CD ARG A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 12 NE ARG A 2 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 13 CZ ARG A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 14 NH1 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 15 NH2 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 16 N GLU A 3 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 17 CA GLU A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 18 C GLU A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 23 OE1 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 24 OE2 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 25 N GLY A 4 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 26 CA GLY A 4 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 27 C GLY A 4 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 28 O GLY A 4 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 29 OXT GLY A 4 0.000 0.000 0.000 1.00 0.00 O 65: CONECT 1 2 65: CONECT 2 3 65: CONECT 3 4 4 5 65: CONECT 5 6 65: CONECT 6 7 9 65: CONECT 7 8 8 16 65: CONECT 9 10 65: CONECT 10 11 65: CONECT 11 12 65: CONECT 12 13 65: CONECT 13 14 14 15 65: CONECT 16 17 65: CONECT 17 18 20 65: CONECT 18 19 19 25 65: CONECT 20 21 65: CONECT 21 22 65: CONECT 22 23 23 24 65: CONECT 25 26 65: CONECT 26 27 65: CONECT 27 28 28 29 65: END 65: 65: Sequence: CYIQNCPLG 65: HELM: PEPTIDE1{C.Y.I.Q.N.C.P.L.G.[am]}$PEPTIDE1,PEPTIDE1,1:R3-6:R3$$$ 65: Smiles: CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccc(O)cc2)NC(=O)[C@@H](N)CSSC[C@@H](C(=O)N2CCC[C@H]2C(=O)N[C@@H](CC(C)C)C(=O)NCC(N)=O)NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](CCC(N)=O)NC1=O 65: PDB: 65: ATOM 1 N CYS A 1 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 2 CA CYS A 1 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 3 C CYS A 1 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 4 O CYS A 1 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 5 CB CYS A 1 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 6 SG CYS A 1 0.000 0.000 0.000 1.00 0.00 S 65: ATOM 7 N TYR A 2 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 8 CA TYR A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 9 C TYR A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 10 O TYR A 2 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 11 CB TYR A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 12 CG TYR A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 13 CD1 TYR A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 14 CD2 TYR A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 15 CE1 TYR A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 16 CE2 TYR A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 17 CZ TYR A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 18 OH TYR A 2 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 19 N ILE A 3 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 20 CA ILE A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 21 C ILE A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 22 O ILE A 3 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 23 CB ILE A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 24 CG1 ILE A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 25 CG2 ILE A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 26 CD1 ILE A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 27 N GLN A 4 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 28 CA GLN A 4 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 29 C GLN A 4 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 30 O GLN A 4 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 31 CB GLN A 4 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 32 CG GLN A 4 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 33 CD GLN A 4 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 34 OE1 GLN A 4 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 35 NE2 GLN A 4 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 36 N ASN A 5 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 37 CA ASN A 5 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 38 C ASN A 5 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 39 O ASN A 5 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 40 CB ASN A 5 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 41 CG ASN A 5 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 42 OD1 ASN A 5 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 43 ND2 ASN A 5 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 44 N CYS A 6 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 45 CA CYS A 6 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 46 C CYS A 6 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 47 O CYS A 6 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 48 CB CYS A 6 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 49 SG CYS A 6 0.000 0.000 0.000 1.00 0.00 S 65: ATOM 50 N PRO A 7 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 51 CA PRO A 7 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 52 C PRO A 7 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 53 O PRO A 7 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 54 CB PRO A 7 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 55 CG PRO A 7 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 56 CD PRO A 7 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 57 N LEU A 8 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 58 CA LEU A 8 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 59 C LEU A 8 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 60 O LEU A 8 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 61 CB LEU A 8 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 62 CG LEU A 8 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 63 CD1 LEU A 8 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 64 CD2 LEU A 8 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 65 N GLY A 9 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 66 CA GLY A 9 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 67 C GLY A 9 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 68 O GLY A 9 0.000 0.000 0.000 1.00 0.00 O 65: HETATM 69 N NH2 A 10 0.000 0.000 0.000 1.00 0.00 N 65: CONECT 1 2 65: CONECT 2 3 5 65: CONECT 3 4 4 7 65: CONECT 5 6 65: CONECT 6 49 65: CONECT 7 8 65: CONECT 8 9 11 65: CONECT 9 10 10 19 65: CONECT 11 12 65: CONECT 12 13 13 14 65: CONECT 13 15 65: CONECT 14 16 16 65: CONECT 15 17 17 65: CONECT 16 17 65: CONECT 17 18 65: CONECT 19 20 65: CONECT 20 21 23 65: CONECT 21 22 22 27 65: CONECT 23 24 25 65: CONECT 25 26 65: CONECT 27 28 65: CONECT 28 29 31 65: CONECT 29 30 30 36 65: CONECT 31 32 65: CONECT 32 33 65: CONECT 33 34 34 35 65: CONECT 36 37 65: CONECT 37 38 40 65: CONECT 38 39 39 44 65: CONECT 40 41 65: CONECT 41 42 42 43 65: CONECT 44 45 65: CONECT 45 46 48 65: CONECT 46 47 47 50 65: CONECT 48 49 65: CONECT 50 51 56 65: CONECT 51 52 54 65: CONECT 52 53 53 57 65: CONECT 54 55 65: CONECT 55 56 65: CONECT 57 58 65: CONECT 58 59 61 65: CONECT 59 60 60 65 65: CONECT 61 62 65: CONECT 62 63 64 65: CONECT 65 66 65: CONECT 66 67 65: CONECT 67 68 68 69 65: END 65: 65: Sequence: LfPVXLfPVX 65: HELM: PEPTIDE1{L.[dF].P.V.[Orn].L.[dF].P.V.[Orn]}$PEPTIDE1,PEPTIDE1,10:R2-1:R1$$$ 65: Smiles: CC(C)C[C@@H]1NC(=O)[C@H](CCCN)NC(=O)[C@H](C(C)C)NC(=O)[C@@H]2CCCN2C(=O)[C@@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC(=O)[C@H](CCCN)NC(=O)[C@H](C(C)C)NC(=O)[C@@H]2CCCN2C(=O)[C@@H](Cc2ccccc2)NC1=O 65: PDB: 65: ATOM 1 N LEU A 1 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 2 CA LEU A 1 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 3 C LEU A 1 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 4 O LEU A 1 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 5 CB LEU A 1 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 6 CG LEU A 1 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 7 CD1 LEU A 1 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 8 CD2 LEU A 1 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 9 N DPN A 2 0.000 0.000 0.000 1.00 0.00 N 65: HETATM 10 CA DPN A 2 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 11 C DPN A 2 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 12 O DPN A 2 0.000 0.000 0.000 1.00 0.00 O 65: HETATM 13 CB DPN A 2 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 14 CG DPN A 2 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 15 CD1 DPN A 2 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 16 CD2 DPN A 2 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 17 CE1 DPN A 2 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 18 CE2 DPN A 2 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 19 CZ DPN A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 20 N PRO A 3 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 21 CA PRO A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 22 C PRO A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 23 O PRO A 3 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 24 CB PRO A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 25 CG PRO A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 26 CD PRO A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 27 N VAL A 4 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 28 CA VAL A 4 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 29 C VAL A 4 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 30 O VAL A 4 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 31 CB VAL A 4 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 32 CG1 VAL A 4 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 33 CG2 VAL A 4 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 34 N ORN A 5 0.000 0.000 0.000 1.00 0.00 N 65: HETATM 35 CA ORN A 5 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 36 C ORN A 5 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 37 O ORN A 5 0.000 0.000 0.000 1.00 0.00 O 65: HETATM 38 CB ORN A 5 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 39 CG ORN A 5 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 40 CD ORN A 5 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 41 NE ORN A 5 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 42 N LEU A 6 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 43 CA LEU A 6 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 44 C LEU A 6 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 45 O LEU A 6 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 46 CB LEU A 6 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 47 CG LEU A 6 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 48 CD1 LEU A 6 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 49 CD2 LEU A 6 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 50 N DPN A 7 0.000 0.000 0.000 1.00 0.00 N 65: HETATM 51 CA DPN A 7 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 52 C DPN A 7 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 53 O DPN A 7 0.000 0.000 0.000 1.00 0.00 O 65: HETATM 54 CB DPN A 7 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 55 CG DPN A 7 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 56 CD1 DPN A 7 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 57 CD2 DPN A 7 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 58 CE1 DPN A 7 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 59 CE2 DPN A 7 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 60 CZ DPN A 7 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 61 N PRO A 8 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 62 CA PRO A 8 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 63 C PRO A 8 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 64 O PRO A 8 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 65 CB PRO A 8 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 66 CG PRO A 8 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 67 CD PRO A 8 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 68 N VAL A 9 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 69 CA VAL A 9 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 70 C VAL A 9 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 71 O VAL A 9 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 72 CB VAL A 9 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 73 CG1 VAL A 9 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 74 CG2 VAL A 9 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 75 N ORN A 10 0.000 0.000 0.000 1.00 0.00 N 65: HETATM 76 CA ORN A 10 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 77 C ORN A 10 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 78 O ORN A 10 0.000 0.000 0.000 1.00 0.00 O 65: HETATM 79 CB ORN A 10 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 80 CG ORN A 10 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 81 CD ORN A 10 0.000 0.000 0.000 1.00 0.00 C 65: HETATM 82 NE ORN A 10 0.000 0.000 0.000 1.00 0.00 N 65: CONECT 1 2 77 65: CONECT 2 3 5 65: CONECT 3 4 4 9 65: CONECT 5 6 65: CONECT 6 7 8 65: CONECT 9 10 65: CONECT 10 11 13 65: CONECT 11 12 12 20 65: CONECT 13 14 65: CONECT 14 15 15 16 65: CONECT 15 17 65: CONECT 16 18 18 65: CONECT 17 19 19 65: CONECT 18 19 65: CONECT 20 21 26 65: CONECT 21 22 24 65: CONECT 22 23 23 27 65: CONECT 24 25 65: CONECT 25 26 65: CONECT 27 28 65: CONECT 28 29 31 65: CONECT 29 30 30 34 65: CONECT 31 32 33 65: CONECT 34 35 65: CONECT 35 36 38 65: CONECT 36 37 37 42 65: CONECT 38 39 65: CONECT 39 40 65: CONECT 40 41 65: CONECT 42 43 65: CONECT 43 44 46 65: CONECT 44 45 45 50 65: CONECT 46 47 65: CONECT 47 48 49 65: CONECT 50 51 65: CONECT 51 52 54 65: CONECT 52 53 53 61 65: CONECT 54 55 65: CONECT 55 56 56 57 65: CONECT 56 58 65: CONECT 57 59 59 65: CONECT 58 60 60 65: CONECT 59 60 65: CONECT 61 62 67 65: CONECT 62 63 65 65: CONECT 63 64 64 68 65: CONECT 65 66 65: CONECT 66 67 65: CONECT 68 69 65: CONECT 69 70 72 65: CONECT 70 71 71 75 65: CONECT 72 73 74 65: CONECT 75 76 65: CONECT 76 77 79 65: CONECT 77 78 78 65: CONECT 79 80 65: CONECT 80 81 65: CONECT 81 82 65: END 65: 65: Sequence: GREG 65: HELM: PEPTIDE1{G.R.E.G}$$$$ 65: Smiles: N=C(N)NCCCC(NC(=O)CN)C(=O)NC(CCC(=O)O)C(=O)NCC(=O)O 65: PDB: 65: ATOM 1 N GLY A 1 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 2 CA GLY A 1 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 3 C GLY A 1 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 4 O GLY A 1 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 5 N ARG A 2 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 6 CA ARG A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 7 C ARG A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 8 O ARG A 2 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 9 CB ARG A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 10 CG ARG A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 11 CD ARG A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 12 NE ARG A 2 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 13 CZ ARG A 2 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 14 NH1 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 15 NH2 ARG A 2 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 16 N GLU A 3 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 17 CA GLU A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 18 C GLU A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 23 OD1 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 24 OD2 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 25 N GLY A 4 0.000 0.000 0.000 1.00 0.00 N 65: ATOM 26 CA GLY A 4 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 27 C GLY A 4 0.000 0.000 0.000 1.00 0.00 C 65: ATOM 28 O GLY A 4 0.000 0.000 0.000 1.00 0.00 O 65: ATOM 29 OXT GLY A 4 0.000 0.000 0.000 1.00 0.00 O 65: CONECT 1 2 65: CONECT 2 3 65: CONECT 3 4 4 5 65: CONECT 5 6 65: CONECT 6 7 9 65: CONECT 7 8 8 16 65: CONECT 9 10 65: CONECT 10 11 65: CONECT 11 12 65: CONECT 12 13 65: CONECT 13 14 14 15 65: CONECT 16 17 65: CONECT 17 18 20 65: CONECT 18 19 19 25 65: CONECT 20 21 65: CONECT 21 22 65: CONECT 22 23 23 24 65: CONECT 25 26 65: CONECT 26 27 65: CONECT 27 28 28 29 65: END 65: 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 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 67: no bonds 67: Violation occurred on line 139 in file ./Code/GraphMol/SubstanceGroup.cpp 67: Failed Expression: !d_bonds.empty() 67: **** 67: 67: [16:02:59] SGroup 3 referenced on line 40 not found. 67: [16:02:59] 67: 67: **** 67: Pre-condition Violation 67: no bonds 67: Violation occurred on line 139 in file ./Code/GraphMol/SubstanceGroup.cpp 67: Failed Expression: !d_bonds.empty() 67: **** 67: 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 67: multiple bonds with same bookmark 67: Violation occurred on line 269 in file ./Code/GraphMol/ROMol.cpp 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: 67: [16:02:59] 67: 67: **** 67: Pre-condition Violation 67: multiple bonds with same bookmark 67: Violation occurred on line 269 in file ./Code/GraphMol/ROMol.cpp 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: 67: [16:02:59] multiple bonds with same bookmark 67: [16:02:59] 67: 67: **** 67: Pre-condition Violation 67: bond is not part of the SubstanceGroup 67: Violation occurred on line 158 in file ./Code/GraphMol/SubstanceGroup.cpp 67: Failed Expression: std::find(d_bonds.begin(), d_bonds.end(), bondIdx) != d_bonds.end() 67: **** 67: 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 67: multiple atoms with same bookmark 67: Violation occurred on line 248 in file ./Code/GraphMol/ROMol.cpp 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: 67: [16:02:59] 67: 67: **** 67: Pre-condition Violation 67: multiple atoms with same bookmark 67: Violation occurred on line 248 in file ./Code/GraphMol/ROMol.cpp 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: 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 67: multiple bonds with same bookmark 67: Violation occurred on line 269 in file ./Code/GraphMol/ROMol.cpp 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: 67: [16:02:59] WARNING: final character of V3000 array is not ')' 67: [16:02:59] 67: 67: **** 67: Pre-condition Violation 67: multiple bonds with same bookmark 67: Violation occurred on line 269 in file ./Code/GraphMol/ROMol.cpp 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: 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 67: multiple atoms with same bookmark 67: Violation occurred on line 248 in file ./Code/GraphMol/ROMol.cpp 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: 67: [16:02:59] WARNING: final character of V3000 array is not ')' 67: [16:02:59] 67: 67: **** 67: Pre-condition Violation 67: multiple atoms with same bookmark 67: Violation occurred on line 248 in file ./Code/GraphMol/ROMol.cpp 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: 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 67: multiple bonds with same bookmark 67: Violation occurred on line 269 in file ./Code/GraphMol/ROMol.cpp 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: 67: [16:02:59] 67: 67: **** 67: Pre-condition Violation 67: multiple bonds with same bookmark 67: Violation occurred on line 269 in file ./Code/GraphMol/ROMol.cpp 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: 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 67: multiple atoms with same bookmark 67: Violation occurred on line 248 in file ./Code/GraphMol/ROMol.cpp 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: 67: [16:02:59] 67: 67: **** 67: Pre-condition Violation 67: multiple atoms with same bookmark 67: Violation occurred on line 248 in file ./Code/GraphMol/ROMol.cpp 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: 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 67: no stream 67: Violation occurred on line 144 in file ./Code/GraphMol/FileParsers/SDMolSupplier.cpp 67: Failed Expression: dp_inStream 67: **** 67: 67: [16:02:59] 67: 67: **** 67: Pre-condition Violation 67: no stream 67: Violation occurred on line 179 in file ./Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp 67: Failed Expression: dp_inStream 67: **** 67: 67: [16:02:59] 67: 67: **** 67: Pre-condition Violation 67: no stream 67: Violation occurred on line 429 in file ./Code/GraphMol/FileParsers/SmilesMolSupplier.cpp 67: Failed Expression: dp_inStream 67: **** 67: 67: [16:02:59] 67: 67: **** 67: Pre-condition Violation 67: no stream 67: Violation occurred on line 274 in file ./Code/GraphMol/FileParsers/TDTMolSupplier.cpp 67: Failed Expression: dp_inStream 67: **** 67: 67: [16:02:59] 67: 67: **** 67: Pre-condition Violation 67: no stream 67: Violation occurred on line 448 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp 67: Failed Expression: dp_sInStream != nullptr 67: **** 67: 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 67: Element '' not found 67: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h 67: Failed Expression: anum > -1 67: **** 67: 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 67: idx 67: Violation occurred on line 324 in file ./Code/GraphMol/ROMol.cpp 67: Failed Expression: 99 < 9 67: **** 67: 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: 61/208 Test #67: fileParsersCatchTest ................... Passed 0.14 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 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 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 71: done 71: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 71: processing2 71: launch2 :0 71: launch2 :1 71: launch2 :2 71: launch2 :3 71: done 71: preprocessing 3 71: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 71: processing3 71: launch3 :0 71: launch3 :1 71: launch3 :2 71: launch3 :3 65/208 Test #39: resMolSupplierTest ..................... Passed 5.77 sec 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 71: done 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 71: matches must not be empty 71: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp 71: Failed Expression: !matches.empty() 71: **** 71: 71: [16:03:00] 71: 71: **** 71: Pre-condition Violation 71: matches must not be empty 71: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp 71: Failed Expression: !matches.empty() 71: **** 71: 66/208 Test #71: testSubstructMatch ..................... Passed 0.49 sec test 73 Start 73: testGenericGroups 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 78: getNumImplicitHs() called without preceding call to calcImplicitValence() 78: Violation occurred on line 297 in file ./Code/GraphMol/Atom.cpp 78: Failed Expression: d_implicitValence > -1 78: **** 78: 78: [16:03:01] 78: 78: **** 78: Pre-condition Violation 78: getNumImplicitHs() called without preceding call to calcImplicitValence() 78: Violation occurred on line 297 in file ./Code/GraphMol/Atom.cpp 78: Failed Expression: d_implicitValence > -1 78: **** 78: 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: [16:03:01] mapped atoms in the reactants were not mapped in the products. 78: unmapped numbers are: 3 78: .[16:03:02] mapped atoms in the reactants were not mapped in the products. 78: unmapped numbers are: 3 78: ../build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:515: DeprecationWarning: Please use assertTrue instead. 78: self.failUnless(rxn) 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: ......[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: [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 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: [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 80: 80: RDKit 80: 80: 2 1 80: $MOL 80: 80: RDKit 2D 80: 80: 2 1 0 0 0 0 0 0 0 0999 V2000 80: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 80: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 80: 1 2 1 0 80: M RGP 1 2 1 80: V 1 halogen.bromine.aromatic 80: V 2 [*:1] 80: M END 80: $MOL 80: 80: RDKit 2D 80: 80: 4 3 0 0 0 0 0 0 0 0999 V2000 80: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 80: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 80: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 80: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 80: 2 3 1 0 80: 1 2 1 0 80: 2 4 1 0 80: M RGP 1 1 2 80: V 1 [*:2] 80: V 2 boronicacid 80: M END 80: $MOL 80: 80: RDKit 2D 80: 80: 2 1 0 0 0 0 0 0 0 0999 V2000 80: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 80: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 80: 1 2 1 0 80: M RGP 2 1 1 2 2 80: V 1 [*:1] 80: V 2 [*:2] 80: M END 80: 80: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 80: $RXN 80: 80: RDKit 80: 80: 2 1 80: $MOL 80: 80: RDKit 2D 80: 80: 2 1 0 0 0 0 0 0 0 0999 V2000 80: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 80: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 80: 1 2 1 0 80: M RGP 1 2 1 80: V 1 halogen.bromine.aromatic 80: V 2 [*:1] 80: M END 80: $MOL 80: 80: RDKit 2D 80: 80: 4 3 0 0 0 0 0 0 0 0999 V2000 80: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 80: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 80: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 80: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 80: 2 3 1 0 80: 1 2 1 0 80: 2 4 1 0 80: M RGP 1 1 2 80: V 1 [*:2] 80: V 2 boronicacid 80: M END 80: $MOL 80: 80: RDKit 2D 80: 80: 2 1 0 0 0 0 0 0 0 0999 V2000 80: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 80: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 80: 1 2 1 0 80: M RGP 2 1 1 2 2 80: V 1 [*:1] 80: V 2 [*:2] 80: M END 80: 80: ******************************************** 80: $RXN 80: 80: RDKit 80: 80: 2 1 80: $MOL 80: 80: RDKit 2D 80: 80: 2 1 0 0 0 0 0 0 0 0999 V2000 80: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 80: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 80: 1 2 1 0 80: M RGP 1 2 1 80: V 1 halogen.bromine.aromatic 80: V 2 * 80: M END 80: $MOL 80: 80: RDKit 2D 80: 80: 4 3 0 0 0 0 0 0 0 0999 V2000 80: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 80: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 80: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 80: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 80: 2 3 1 0 80: 1 2 1 0 80: 2 4 1 0 80: M RGP 1 1 2 80: V 1 * 80: V 2 boronicacid 80: M END 80: $MOL 80: 80: RDKit 2D 80: 80: 2 1 0 0 0 0 0 0 0 0999 V2000 80: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 80: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0 80: 1 2 1 0 80: M RGP 2 1 1 2 2 80: V 1 * 80: V 2 * 80: M END 80: 80: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 80: $RXN 80: 80: RDKit 80: 80: 2 1 80: $MOL 80: 80: RDKit 2D 80: 80: 2 1 0 0 0 0 0 0 0 0999 V2000 80: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 80: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 80: 1 2 1 0 80: M RGP 1 2 1 80: V 1 halogen.bromine.aromatic 80: V 2 [*:1] 80: M END 80: $MOL 80: 80: RDKit 2D 80: 80: 4 3 0 0 0 0 0 0 0 0999 V2000 80: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 80: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 80: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 80: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 80: 2 3 1 0 80: 1 2 1 0 80: 2 4 1 0 80: M RGP 1 1 2 80: V 1 [*:2] 80: V 2 boronicacid 80: M END 80: $MOL 80: 80: RDKit 2D 80: 80: 2 1 0 0 0 0 0 0 0 0999 V2000 80: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 80: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 80: 1 2 1 0 80: M RGP 2 1 1 2 2 80: V 1 [*:1] 80: V 2 [*:2] 80: M END 80: 80: ******************************************** 80: $RXN 80: 80: RDKit 80: 80: 2 1 80: $MOL 80: 80: RDKit 2D 80: 80: 2 1 0 0 0 0 0 0 0 0999 V2000 80: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 80: -3.9875 -7.4667 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 80: 1 2 1 0 80: V 1 halogen.bromine.aromatic 80: M END 80: $MOL 80: 80: RDKit 2D 80: 80: 4 3 0 0 0 0 0 0 0 0999 V2000 80: 3.4375 -7.7917 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 80: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 80: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 80: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 80: 2 3 1 0 80: 1 2 1 0 80: 2 4 1 0 80: V 2 boronicacid 80: M END 80: $MOL 80: 80: RDKit 2D 80: 80: 2 1 0 0 0 0 0 0 0 0999 V2000 80: 11.2667 -7.3417 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 80: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 80: 1 2 1 0 80: M END 80: 80: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 80: $RXN 80: 80: RDKit 80: 80: 2 1 80: $MOL 80: 80: RDKit 2D 80: 80: 2 1 0 0 0 0 0 0 0 0999 V2000 80: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 80: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 80: 1 2 1 0 80: M RGP 1 2 1 80: V 1 halogen.bromine.aromatic 80: V 2 [*:1] 80: M END 80: $MOL 80: 80: RDKit 2D 80: 80: 4 3 0 0 0 0 0 0 0 0999 V2000 80: 3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 80: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 80: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 80: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 80: 2 3 1 0 80: 1 2 1 0 80: 2 4 1 0 80: M RGP 1 1 2 80: V 1 [*:2] 80: V 2 boronicacid 80: M END 80: $MOL 80: 80: RDKit 2D 80: 80: 2 1 0 0 0 0 0 0 0 0999 V2000 80: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 80: 11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0 80: 1 2 1 0 80: M RGP 2 1 1 2 2 80: V 1 [*:1] 80: V 2 [*:2] 80: M END 80: 80: ******************************************** 80: $RXN 80: 80: RDKit 80: 80: 2 1 80: $MOL 80: 80: RDKit 2D 80: 80: 2 1 0 0 0 0 0 0 0 0999 V2000 80: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 80: -3.9875 -7.4667 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 80: 1 2 1 0 80: V 1 halogen.bromine.aromatic 80: M END 80: $MOL 80: 80: RDKit 2D 80: 80: 4 3 0 0 0 0 0 0 0 0999 V2000 80: 3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0 80: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 80: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 80: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 80: 2 3 1 0 80: 1 2 1 0 80: 2 4 1 0 80: V 2 boronicacid 80: M END 80: $MOL 80: 80: RDKit 2D 80: 80: 2 1 0 0 0 0 0 0 0 0999 V2000 80: 11.2667 -7.3417 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0 80: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 80: 1 2 1 0 80: M END 80: 80: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 80: .. 80: ---------------------------------------------------------------------- 80: Ran 4 tests in 0.030s 80: 80: OK 80: $RXN 80: 80: RDKit 80: 80: 2 1 80: $MOL 80: 80: RDKit 2D 80: 80: 2 1 0 0 0 0 0 0 0 0999 V2000 80: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 80: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 80: 1 2 1 0 80: M RGP 1 2 1 80: V 1 halogen.bromine.aromatic 80: V 2 [*:1] 80: M END 80: $MOL 80: 80: RDKit 2D 80: 80: 4 3 0 0 0 0 0 0 0 0999 V2000 80: 3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0 80: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 80: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 80: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 80: 2 3 1 0 80: 1 2 1 0 80: 2 4 1 0 80: V 2 boronicacid 80: M END 80: $MOL 80: 80: RDKit 2D 80: 80: 2 1 0 0 0 0 0 0 0 0999 V2000 80: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 80: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 80: 1 2 1 0 80: M RGP 1 1 1 80: V 1 [*:1] 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 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 86: ----------------------- 86: Test1: pathToSubmol 86: Finished 86: ----------------------- 86: Test2: Atom Environments 86: Finished 86: ----------------------- 86: Test 3: Atom Environments (Extension) 86: Finished 86: ----------------------- 86: Testing github Issue103: stereochemistry and pathToSubmol 86: Finished 86: ----------------------- 86: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) 86: Finished 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 85: Finished 85: ----------------------- 85: Path retrieval 85: Finished 85: ----------------------- 85: Path retrieval2 85: Finished 85: ----------------------- 85: Unique Subgraph retrieval 85: Finished 85: ----------------------- 85: testUniqueSubgraphs2 87: Warning: molecule failed filter 87: Warning: molecule failed filter: reason hzone_phenol_A(479) 87: v = { 87: 0,23}, 87: 1,22}, 87: 2,20}, 87: 3,19}, 87: 4,25}, 87: 5,24}, 87: 6,18}, 87: 7,17}, 87: 8,16}, 87: 9,21}, 87: } 87: match = { 87: 0,23}, 87: 1,22}, 87: 2,20}, 87: 3,19}, 87: 4,25}, 87: 5,24}, 87: 6,18}, 87: 7,17}, 87: 8,16}, 87: 9,21}, 87: } 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 = { 87: 0,11}, 87: 1,12}, 87: 2,13}, 87: 3,14}, 87: 4,15}, 87: 5,10}, 87: 6,9}, 87: 7,8}, 87: 8,7}, 87: 9,6}, 87: 10,5}, 87: 11,17}, 87: 12,16}, 87: } 87: match = { 87: 0,11}, 87: 1,12}, 87: 2,13}, 87: 3,14}, 87: 4,15}, 87: 5,10}, 87: 6,9}, 87: 7,8}, 87: 8,7}, 87: 9,6}, 87: 10,5}, 87: 11,17}, 87: 12,16}, 87: } 81/208 Test #61: testMultithreadedMolSupplier ........... Passed 7.47 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 87: Warning: molecule failed filter 87: Warning: molecule failed filter: reason keto_keto_gamma(5) 87: v = { 87: 0,0}, 87: 1,1}, 87: 2,2}, 87: 3,4}, 87: 4,5}, 87: 5,6}, 87: 6,7}, 87: 7,8}, 87: 8,9}, 87: 9,14}, 87: 10,15}, 87: 11,16}, 87: } 87: match = { 87: 0,0}, 87: 1,1}, 87: 2,2}, 87: 3,4}, 87: 4,5}, 87: 5,6}, 87: 6,7}, 87: 7,8}, 87: 8,9}, 87: 9,14}, 87: 10,15}, 87: 11,16}, 87: } 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 87: 0 hzone_phenol_A(479) 87: 1 cyano_imine_B(17) 87: 2 keto_keto_gamma(5) 82/208 Test #87: filterCatalogTest ...................... Passed 0.24 sec test 89 Start 89: testFragCatalog 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 85: Finished 85: ----------------------- 85: testRootedPaths 85: Finished 83/208 Test #85: testSubgraphs1 ......................... Passed 0.51 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 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 0.117s 90: 90: OK 84/208 Test #90: pyFragCatalog .......................... Passed 0.52 sec test 91 Start 91: testDescriptors 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 89: nonsense 89: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp 89: Failed Expression: token != tokens.end() 89: **** 89: 89: [16:03:07] 89: 89: **** 89: Invariant Violation 89: nonsense no new line 89: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp 89: Failed Expression: token != tokens.end() 89: **** 89: 89: [16:03:07] 89: 89: **** 89: Invariant Violation 89: nonsense with tab 89: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp 89: Failed Expression: token != tokens.end() 89: **** 89: 85/208 Test #89: testFragCatalog ........................ Passed 0.96 sec test 92 Start 92: testAUTOCORR2D 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 1.134s 88: 88: OK 88: (Five aromatic carbons And (Not any of Five aromatic carbons)) 88: (Five aromatic carbons Or (Not any of Five aromatic carbons)) 88: (Not (Five aromatic carbons And (Not any of Five aromatic carbons))) 88: ******************************************** 88: Testing: PAINS_A 2 88: ******************************************** 88: Testing: PAINS_B 4 88: ******************************************** 88: Testing: PAINS_C 8 88: ******************************************** 88: Testing: PAINS 14 88: (Not FilterMatcher) 88: Bar 88: Count 1 88: ******************************************** 88: {'Cl,Br,I'} 88: 1 88: 2 88: running 86/208 Test #88: pyFilterCatalog ........................ Passed 1.46 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 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: 0.902273 s 95: Errors:0 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 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 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 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 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 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 105: =============================================================================== 105: All tests passed (130 assertions in 5 test cases) 105: 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 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 108: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints 108: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints 108: Test timeout computed to be: 1500 108: 108: 108: 108: 108: 108: 108: 108: 108: 108: ------------------- 108: 108: 108: 108: 108: 108: 108: 108: 108: 108: ------------------- 108: Atoms: 108: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 108: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 108: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: Bonds: 108: 0 0->1 order: 1 conj?: 1 aromatic?: 0 108: 1 1->2 order: 12 conj?: 1 aromatic?: 1 108: 2 2->3 order: 12 conj?: 1 aromatic?: 1 108: 3 3->4 order: 12 conj?: 1 aromatic?: 1 108: 4 4->5 order: 12 conj?: 1 aromatic?: 1 108: 5 5->6 order: 12 conj?: 1 aromatic?: 1 108: 6 6->7 order: 12 conj?: 1 aromatic?: 1 108: 7 7->8 order: 12 conj?: 1 aromatic?: 1 108: 8 8->9 order: 1 conj?: 1 aromatic?: 0 108: 9 8->10 order: 12 conj?: 1 aromatic?: 1 108: 10 10->1 order: 12 conj?: 1 aromatic?: 1 108: 11 7->3 order: 12 conj?: 1 aromatic?: 1 108: 108: 108: 108: 108: 108: 108: 108: 108: 108: ------------------- 108: SMI: Oc1cc2[nH]cnc2c(O)n1 108: Atoms: 108: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 108: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 108: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: Bonds: 108: 0 0->1 order: 1 conj?: 1 aromatic?: 0 108: 1 1->2 order: 12 conj?: 1 aromatic?: 1 108: 2 2->3 order: 12 conj?: 1 aromatic?: 1 108: 3 3->4 order: 12 conj?: 1 aromatic?: 1 108: 4 4->5 order: 12 conj?: 1 aromatic?: 1 108: 5 5->6 order: 12 conj?: 1 aromatic?: 1 108: 6 6->7 order: 12 conj?: 1 aromatic?: 1 108: 7 7->8 order: 12 conj?: 1 aromatic?: 1 108: 8 8->9 order: 1 conj?: 1 aromatic?: 0 108: 9 8->10 order: 12 conj?: 1 aromatic?: 1 108: 10 10->1 order: 12 conj?: 1 aromatic?: 1 108: 11 7->3 order: 12 conj?: 1 aromatic?: 1 108: 108: 108: 108: 108: 108: 108: 108: 108: 108: ------------------- 108: 108: SMI: c1(O)cc2[nH]cnc2c(O)n1 108: Atoms: 108: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 1 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 108: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 108: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: Bonds: 108: 0 0->1 order: 1 conj?: 1 aromatic?: 0 108: 1 0->2 order: 12 conj?: 1 aromatic?: 1 108: 2 2->3 order: 12 conj?: 1 aromatic?: 1 108: 3 3->4 order: 12 conj?: 1 aromatic?: 1 108: 4 4->5 order: 12 conj?: 1 aromatic?: 1 108: 5 5->6 order: 12 conj?: 1 aromatic?: 1 108: 6 6->7 order: 12 conj?: 1 aromatic?: 1 108: 7 7->8 order: 12 conj?: 1 aromatic?: 1 108: 8 8->9 order: 1 conj?: 1 aromatic?: 0 108: 9 8->10 order: 12 conj?: 1 aromatic?: 1 108: 10 10->0 order: 12 conj?: 1 aromatic?: 1 108: 11 7->3 order: 12 conj?: 1 aromatic?: 1 108: 108: 108: 108: 108: 108: 108: 108: 108: 108: ------------------- 108: 108: SMI: c1c(O)nc(O)c2c1[nH]cn2 108: Atoms: 108: 0 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 2 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 108: 3 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 5 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 108: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: Bonds: 108: 0 0->1 order: 12 conj?: 1 aromatic?: 1 108: 1 1->2 order: 1 conj?: 1 aromatic?: 0 108: 2 1->3 order: 12 conj?: 1 aromatic?: 1 108: 3 3->4 order: 12 conj?: 1 aromatic?: 1 108: 4 4->5 order: 1 conj?: 1 aromatic?: 0 108: 5 4->6 order: 12 conj?: 1 aromatic?: 1 108: 6 6->7 order: 12 conj?: 1 aromatic?: 1 108: 7 7->8 order: 12 conj?: 1 aromatic?: 1 108: 8 8->9 order: 12 conj?: 1 aromatic?: 1 108: 9 9->10 order: 12 conj?: 1 aromatic?: 1 108: 10 7->0 order: 12 conj?: 1 aromatic?: 1 108: 11 10->6 order: 12 conj?: 1 aromatic?: 1 108: 108: 108: 108: 108: 108: 108: 108: 108: 108: ------------------- 108: 108: SMI: c12cc(O)nc(O)c1nc[nH]2 108: Atoms: 108: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 3 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 108: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 108: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: Bonds: 108: 0 0->1 order: 12 conj?: 1 aromatic?: 1 108: 1 1->2 order: 12 conj?: 1 aromatic?: 1 108: 2 2->3 order: 1 conj?: 1 aromatic?: 0 108: 3 2->4 order: 12 conj?: 1 aromatic?: 1 108: 4 4->5 order: 12 conj?: 1 aromatic?: 1 108: 5 5->6 order: 1 conj?: 1 aromatic?: 0 108: 6 5->7 order: 12 conj?: 1 aromatic?: 1 108: 7 7->8 order: 12 conj?: 1 aromatic?: 1 108: 8 8->9 order: 12 conj?: 1 aromatic?: 1 108: 9 9->10 order: 12 conj?: 1 aromatic?: 1 108: 10 7->0 order: 12 conj?: 1 aromatic?: 1 108: 11 10->0 order: 12 conj?: 1 aromatic?: 1 108: 108: 108: 108: 108: 108: 108: 108: 108: 108: ------------------- 108: 108: SMI: [nH]1c2cc(O)nc(O)c2nc1 108: Atoms: 108: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 4 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 108: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 7 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 108: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 9 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 10 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: Bonds: 108: 0 0->1 order: 12 conj?: 1 aromatic?: 1 108: 1 1->2 order: 12 conj?: 1 aromatic?: 1 108: 2 2->3 order: 12 conj?: 1 aromatic?: 1 108: 3 3->4 order: 1 conj?: 1 aromatic?: 0 108: 4 3->5 order: 12 conj?: 1 aromatic?: 1 108: 5 5->6 order: 12 conj?: 1 aromatic?: 1 108: 6 6->7 order: 1 conj?: 1 aromatic?: 0 108: 7 6->8 order: 12 conj?: 1 aromatic?: 1 108: 8 8->9 order: 12 conj?: 1 aromatic?: 1 108: 9 9->10 order: 12 conj?: 1 aromatic?: 1 108: 10 10->0 order: 12 conj?: 1 aromatic?: 1 108: 11 8->1 order: 12 conj?: 1 aromatic?: 1 108: 108: 108: 108: 108: 108: 108: 108: 108: 108: ------------------- 108: 108: SMI: c1[nH]c2cc(O)nc(O)c2n1 108: Atoms: 108: 0 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: 1 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 3 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 5 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 108: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 8 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 108: 9 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: Bonds: 108: 0 0->1 order: 12 conj?: 1 aromatic?: 1 108: 1 1->2 order: 12 conj?: 1 aromatic?: 1 108: 2 2->3 order: 12 conj?: 1 aromatic?: 1 108: 3 3->4 order: 12 conj?: 1 aromatic?: 1 108: 4 4->5 order: 1 conj?: 1 aromatic?: 0 108: 5 4->6 order: 12 conj?: 1 aromatic?: 1 108: 6 6->7 order: 12 conj?: 1 aromatic?: 1 108: 7 7->8 order: 1 conj?: 1 aromatic?: 0 108: 8 7->9 order: 12 conj?: 1 aromatic?: 1 108: 9 9->10 order: 12 conj?: 1 aromatic?: 1 108: 10 10->0 order: 12 conj?: 1 aromatic?: 1 108: 11 9->2 order: 12 conj?: 1 aromatic?: 1 108: 108: 108: 108: 108: 108: 108: 108: 108: 108: ------------------- 108: 108: SMI: n1c[nH]c2cc(O)nc(O)c21 108: Atoms: 108: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 108: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 108: 10 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: Bonds: 108: 0 0->1 order: 12 conj?: 1 aromatic?: 1 108: 1 1->2 order: 12 conj?: 1 aromatic?: 1 108: 2 2->3 order: 12 conj?: 1 aromatic?: 1 108: 3 3->4 order: 12 conj?: 1 aromatic?: 1 108: 4 4->5 order: 12 conj?: 1 aromatic?: 1 108: 5 5->6 order: 1 conj?: 1 aromatic?: 0 108: 6 5->7 order: 12 conj?: 1 aromatic?: 1 108: 7 7->8 order: 12 conj?: 1 aromatic?: 1 108: 8 8->9 order: 1 conj?: 1 aromatic?: 0 108: 9 8->10 order: 12 conj?: 1 aromatic?: 1 108: 10 10->0 order: 12 conj?: 1 aromatic?: 1 108: 11 10->3 order: 12 conj?: 1 aromatic?: 1 108: 108: 108: 108: 108: 108: 108: 108: 108: 108: ------------------- 108: 108: SMI: c12c(cc(O)nc1O)[nH]cn2 108: Atoms: 108: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 4 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 108: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 7 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 108: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: Bonds: 108: 0 0->1 order: 12 conj?: 1 aromatic?: 1 108: 1 1->2 order: 12 conj?: 1 aromatic?: 1 108: 2 2->3 order: 12 conj?: 1 aromatic?: 1 108: 3 3->4 order: 1 conj?: 1 aromatic?: 0 108: 4 3->5 order: 12 conj?: 1 aromatic?: 1 108: 5 5->6 order: 12 conj?: 1 aromatic?: 1 108: 6 6->7 order: 1 conj?: 1 aromatic?: 0 108: 7 1->8 order: 12 conj?: 1 aromatic?: 1 108: 8 8->9 order: 12 conj?: 1 aromatic?: 1 108: 9 9->10 order: 12 conj?: 1 aromatic?: 1 108: 10 6->0 order: 12 conj?: 1 aromatic?: 1 108: 11 10->0 order: 12 conj?: 1 aromatic?: 1 108: 108: 108: 108: 108: 108: 108: 108: 108: 108: ------------------- 108: 108: SMI: c1(O)c2c(cc(O)n1)[nH]cn2 108: Atoms: 108: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 1 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 108: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 108: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: Bonds: 108: 0 0->1 order: 1 conj?: 1 aromatic?: 0 108: 1 0->2 order: 12 conj?: 1 aromatic?: 1 108: 2 2->3 order: 12 conj?: 1 aromatic?: 1 108: 3 3->4 order: 12 conj?: 1 aromatic?: 1 108: 4 4->5 order: 12 conj?: 1 aromatic?: 1 108: 5 5->6 order: 1 conj?: 1 aromatic?: 0 108: 6 5->7 order: 12 conj?: 1 aromatic?: 1 108: 7 3->8 order: 12 conj?: 1 aromatic?: 1 108: 8 8->9 order: 12 conj?: 1 aromatic?: 1 108: 9 9->10 order: 12 conj?: 1 aromatic?: 1 108: 10 7->0 order: 12 conj?: 1 aromatic?: 1 108: 11 10->2 order: 12 conj?: 1 aromatic?: 1 108: 108: 108: 108: 108: 108: 108: 108: 108: 108: ------------------- 108: 108: SMI: Oc1c2c(cc(O)n1)[nH]cn2 108: Atoms: 108: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 108: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 108: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: Bonds: 108: 0 0->1 order: 1 conj?: 1 aromatic?: 0 108: 1 1->2 order: 12 conj?: 1 aromatic?: 1 108: 2 2->3 order: 12 conj?: 1 aromatic?: 1 108: 3 3->4 order: 12 conj?: 1 aromatic?: 1 108: 4 4->5 order: 12 conj?: 1 aromatic?: 1 108: 5 5->6 order: 1 conj?: 1 aromatic?: 0 108: 6 5->7 order: 12 conj?: 1 aromatic?: 1 108: 7 3->8 order: 12 conj?: 1 aromatic?: 1 108: 8 8->9 order: 12 conj?: 1 aromatic?: 1 108: 9 9->10 order: 12 conj?: 1 aromatic?: 1 108: 10 7->1 order: 12 conj?: 1 aromatic?: 1 108: 11 10->2 order: 12 conj?: 1 aromatic?: 1 108: 108: 108: 108: 108: 108: 108: 108: 108: 108: ------------------- 108: 108: SMI: n1c(O)cc2[nH]cnc2c1O 108: Atoms: 108: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 2 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 108: 3 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 6 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 9 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 10 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 108: Bonds: 108: 0 0->1 order: 12 conj?: 1 aromatic?: 1 108: 1 1->2 order: 1 conj?: 1 aromatic?: 0 108: 2 1->3 order: 12 conj?: 1 aromatic?: 1 108: 3 3->4 order: 12 conj?: 1 aromatic?: 1 108: 4 4->5 order: 12 conj?: 1 aromatic?: 1 108: 5 5->6 order: 12 conj?: 1 aromatic?: 1 108: 6 6->7 order: 12 conj?: 1 aromatic?: 1 108: 7 7->8 order: 12 conj?: 1 aromatic?: 1 108: 8 8->9 order: 12 conj?: 1 aromatic?: 1 108: 9 9->10 order: 1 conj?: 1 aromatic?: 0 108: 10 9->0 order: 12 conj?: 1 aromatic?: 1 108: 11 8->4 order: 12 conj?: 1 aromatic?: 1 108: 108: 108: 108: 108: 108: 108: 108: 108: 108: ------------------- 108: 108: 108: 108: 108: 108: 108: 108: 108: 108: 108: ------------------- 108: 108: 108: 108: 108: 108: 108: 108: 108: 108: ------------------- 108: 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 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: [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 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 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 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 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 108/208 Test #114: testPartialCharges ..................... Passed 0.03 sec test 115 Start 115: pyPartialCharges 115: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py" 115: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/Wrap 115: Test timeout computed to be: 1500 113: . 113: ---------------------------------------------------------------------- 113: Ran 1 test in 0.044s 113: 113: OK 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 116: *********************************************************** 116: Testing MolTransforms 116: --------------------------------- 116: test1Canonicalization 116: 116: --------------------------------- 116: testGetSetBondLength 116: 116: --------------------------------- 116: testGetSetAngle 116: 116: --------------------------------- 116: testGetSetDihedral 116: 116: --------------------------------- 116: testGetSetDihedralThroughTripleBond 116: 116: --------------------------------- 116: testGithub1262: PMI descriptors incorrect 116: 116: --------------------------------- 116: testGithub1908: CanonicalizeMol() distorting bond lengths 116: 116: --------------------------------- 116: testGithub4302: native computeCanonicalTransform() generates non-canonical coords 116: 116: --------------------------------- 116: testWeightedCentroid 116: 116: *********************************************************** 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 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 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 :1 119: launch :2 119: launch :3 119: launch :4 119: launch :5 119: launch :6 119: launch :7 119: launch :8 119: launch :9 119: launch :10 119: launch :11 119: launch :12 119: launch :13 119: launch :14 119: launch :15 119: launch :16 119: launch :17 119: launch :18 119: launch :19 119: launch :20 119: launch :21 119: launch :22 119: 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 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 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. 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 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 123: go 123: ------------------------------------- 123: 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 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 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 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: --------------------------------- 126: test1MolAlign 126: 126: --------------------------------- 126: test1GetBestRMS 126: 126: --------------------------------- 126: test1MolWithQueryAlign 126: 126: --------------------------------- 126: test2AtomMap 126: 126: --------------------------------- 126: test3Weights 126: 126: --------------------------------- 126: testIssue241 126: 126: *********************************************************** 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 128: =============================================================================== 128: All tests passed (9 assertions in 1 test case) 128: 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 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 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: [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 130: molecule has no conformers 130: Violation occurred on line 37 in file ./Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp 130: Failed Expression: dp_mol->getNumConformers() 130: **** 130: 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 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: .[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)) 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 0.131s 131: 131: OK 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 132: *********************************************************** 132: Testing ShapeHelpers 132: --------------------------------- 132: test1Encode 132: 132: --------------------------------- 132: test2Compare 132: 132: --------------------------------- 132: testGithub4364 132: 132: *********************************************************** 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 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 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 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 136: ----------------- Test 1 136: 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 136: ----------------- Test 2 136: file test2_1.png gave hash 2637189532U not the expected 2505713963U 136: file test2_2.png gave hash 2877988061U not the expected 4058920248U 136: Done 136: ----------------- Test 4 136: file test4_1.png gave hash 747479389U not the expected 1924202631U 136: Done 136: ----------------- Test 5 136: file test5_1.png gave hash 1284534124U not the expected 2116545562U 136: file test5_2.png gave hash 1548238783U not the expected 1519942634U 136: file test5_3.png gave hash 2001032737U not the expected 3266389887U 136: Done 136: ----------------- Test 6 (atom labels) 136: Done 136: ----------------- Test 7 (backgrounds) 136: file test7_1.png gave hash 2952006174U not the expected 3331950391U 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 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 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 138: ----------------- Test 1 138: file rxn_test1_1.png gave hash 410482668U not the expected 3579100589U 138: file rxn_test1_2.png gave hash 3429731987U not the expected 3996724834U 138: file rxn_test1_3.png gave hash 645713784U not the expected 4153817948U 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 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 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 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 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 138: file rxn_test2_2_2.png gave hash 3205071265U not the expected 2090979640U 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 138: file rxn_test2_2_3.png gave hash 3292764551U not the expected 857100114U 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 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 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! 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 139: molecule must not be None 139: Violation occurred on line 403 in file ./Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp 139: Failed Expression: m 139: **** 139: 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 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 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 142: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Test/FMCStest 142: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Test 142: Test timeout computed to be: 1500 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_100_15113.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_100_16613.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_100_30745.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_100_30861.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_100_31495.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_100_34869.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_100_36158.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_100_36559.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_100_37434.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_100_39147.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_100_43754.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_100_44011.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_100_44158.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_100_48076.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_100_48961.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_100_49648.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_100_49703.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_100_51128.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_100_51343.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_100_51842.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_100_54554.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_100_55749.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10188_17256.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10188_20244.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10188_20245.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10188_30149.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10188_30499.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10188_36186.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10188_39262.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10188_43966.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10188_45279.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10188_48029.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10188_49064.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10188_49801.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10188_50681.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10188_54039.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10188_58265.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10188_58358.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10188_58866.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10188_60810.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_21358.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_21597.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_30111.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_30349.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_31746.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_31822.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_35220.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_37603.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_37964.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_39508.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_42164.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_42577.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_44072.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_45522.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_46700.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_46719.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_46744.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_48517.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_49087.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_50034.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_51475.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_53483.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_53506.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_54598.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_55614.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_55737.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_57090.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_57705.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_57785.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_58463.txt 142: 142: testChEMBfopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: L_Txt() chembl_II_sets/Target_no_10193_58700.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_61003.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10193_61349.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10260_38526.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10260_50778.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10260_52179.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10260_54285.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10280_30224.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10280_31222.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37349.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37369.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37465.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10280_37541.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10280_38371.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10280_44314.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10280_44578.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10280_45765.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10280_46281.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10280_47928.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10280_50624.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10280_51341.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10280_51662.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10280_51767.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10280_53081.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10280_53396.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10280_53407.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10280_58823.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10280_59190.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10280_60672.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10280_61176.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10434_20905.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10434_30074.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10434_30175.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10434_30423.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10434_31555.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10434_34878.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10434_35926.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10434_42168.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_107_20859.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_107_30060.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_107_30061.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_107_30606.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_107_30866.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_107_31249.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_107_34921.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_107_35188.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_107_36636.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_107_37466.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_107_39202.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_107_43952.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_107_49345.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_107_49591.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_107_49854.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_107_51416.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_107_53537.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_107_58879.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_107_60679.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_107_61269.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_108_20600.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_108_20859.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_108_30060.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_108_30606.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_108_30866.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_108_31558.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_108_35188.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_108_37466.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_108_43875.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_108_48911.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_108_49591.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_108_49854.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: no_108_57887.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_108_60679.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_108_6857.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10980_15478.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10980_20853.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30840.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30862.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30918.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10980_30994.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10980_31014.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10980_31508.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10980_31623.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35003.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35004.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35281.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10980_35957.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10980_36520.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10980_36641.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10980_38586.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10980_44431.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10980_45093.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10980_51302.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10980_5247.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10980_52937.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10980_57198.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10980_5739.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_10980_6535.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11140_20205.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11140_20986.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11140_30091.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11140_34698.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11140_34705.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11140_37038.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11140_37272.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11140_37447.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11140_38909.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11140_38953.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11140_39472.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11140_45825.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11140_47179.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11140_49028.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11140_49860.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11140_51984.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11140_53395.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11140_53826.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11140_54121.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11140_54530.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11140_55738.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11140_57725.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11140_58590.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11365_20432.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11365_30331.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11365_37956.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11365_48114.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11365_58566.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11489_34731.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11489_34818.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11489_37318.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11489_37339.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11489_37564.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11489_39504.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11489_39561.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11489_46082.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11489_46089.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11489_47349.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11489_47757.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11489_51593.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11489_54754.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11489_58262.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11489_58958.txt 142: 142: testChEMBL_Txt(fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: ) chembl_II_sets/Target_no_114_16827.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_20503.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_20724.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_30254.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_30321.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_30572.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_31116.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_31281.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_31443.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_34747.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_34920.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_35040.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_36623.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_37136.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_37208.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_38298.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_38554.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_39088.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_39543.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_44049.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_44562.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_45180.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_45867.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_46087.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_46829.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_47546.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_48395.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_50461.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_50765.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_51669.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_52381.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_57231.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_114_58246.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11534_30999.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11534_31021.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11534_31650.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11534_35011.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11534_37014.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11534_44598.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11534_48446.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11534_50614.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11534_50615.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11534_50618.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11534_51950.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11575_31616.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11575_38381.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11575_45757.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11575_46816.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11575_50701.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11575_54049.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11575_57890.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11575_61045.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11631_30194.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11631_31421.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11631_35538.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11631_55727.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11631_60676.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11631_61130.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_11631_6444.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_15623.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_20096.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_21591.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_30184.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_30380.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_30745.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_30861.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_31619.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_34869.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_35284.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_36158.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_36915.txt 142: 142: testChEMBL_Txfopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: t() chembl_II_sets/Target_no_121_37434.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_37541.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_37677.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_38837.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_39530.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_43793.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_44158.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_44164.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_44579.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_44593.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_44692.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_44914.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_45878.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_48050.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_48706.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_48944.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_48961.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_49880.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_50055.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_50512.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_51064.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_53537.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_55749.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_58879.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_121_6876.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12209_44664.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12209_46451.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12209_50640.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12209_56102.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12209_58015.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12209_59089.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12209_59092.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12209_61340.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12252_31458.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12252_38481.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12252_42104.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12252_49475.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12252_49933.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12252_50558.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_126_37249.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_126_39117.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_126_48227.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_126_48229.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_126_53969.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_126_54262.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_126_55353.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_126_61212.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20250.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20506.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20626.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12952_20689.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12952_21358.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12952_30158.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12952_30349.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12952_34843.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12952_35220.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12952_36318.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12952_36800.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12952_39349.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12952_45385.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12952_45676.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12952_46700.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12952_46719.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12952_48517.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12952_52690.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12952_53483.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12952_55435.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12952_56102.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12952_58015.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_12952_58375.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_1295fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: 2_58700.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_13001_16724.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_13001_2710.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_13001_30128.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_13001_31250.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_13001_35519.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_13001_36905.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_13001_46788.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_13001_4737.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_13001_55736.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_13001_57473.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_16146.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_30313.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_30539.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_30653.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_30988.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_31179.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_31339.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_3525.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_36886.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_37020.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_38128.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_43952.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_45210.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_45899.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_47889.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_51800.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_53158.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_5330.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_55648.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_56096.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_57287.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_57399.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_57606.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_58470.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_130_60894.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_15010.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_20304.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_20542.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_20788.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_21358.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_30349.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_31103.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_31764.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_31822.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_35220.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_37964.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_42164.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_44072.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_45522.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_46719.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_46744.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_48416.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_49740.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_50034.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_50640.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_53483.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_53506.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_53814.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_55435.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_56074.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_56107.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_57090.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_57705.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_57785.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_57861.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_58583.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_59089.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_15_59092.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_20600.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_30764.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_34876.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_37427.tfopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: xt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_38266.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_45283.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_46990.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_47123.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_47900.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_48050.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_48062.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_48076.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_50718.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_50972.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_51372.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_51830.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_53049.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_53505.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_54021.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_54565.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_54570.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_57666.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_57890.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_58072.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_58634.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_58643.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_59080.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_59202.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_59346.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_60379.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_60385.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_165_61098.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_17045_31154.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_17045_35648.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_17045_48914.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_17045_51975.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_17045_52435.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_17045_55790.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_17045_58958.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_17045_61146.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20191.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20562.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20606.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_20607.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30003.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30402.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30726.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_30924.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31457.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31460.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31600.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31620.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31640.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31782.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31797.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31829.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_31856.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_34690.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_34691.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_34694.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_35712.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_37497.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_37539.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48070.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48219.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48824.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_48902.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_52867.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_53534.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_54570.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_58727.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_60159.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_19905_60661.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_30037.txt 142: 142: testChEMBL_Txt() chefopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: mbl_II_sets/Target_no_259_34734.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_35365.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_35787.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_36793.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_37845.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_38328.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_39374.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_43936.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_44059.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_44405.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_44424.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_45166.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_46158.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_46425.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_47187.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_48435.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_48817.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_48849.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_48957.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_48965.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_49519.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_49921.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_50392.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_50972.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_52405.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_52442.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_53169.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_54640.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_57207.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_58537.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_58920.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_259_60358.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_25_16077.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_25_34943.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_25_36391.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_25_36574.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_25_52906.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_25_54642.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_43_16385.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_43_20333.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_43_20774.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_43_35825.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_43_37637.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_43_47741.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_43_48567.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_43_48841.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_43_49589.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_43_50564.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_43_51201.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_43_53150.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_43_55747.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_43_58276.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_51_20813.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_51_2331.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_51_2391.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_51_30374.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_51_30512.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_51_30796.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_51_31058.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_51_31450.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_51_36609.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_51_36636.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_51_38266.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_51_43800.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_51_47621.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_51_49433.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_51_49550.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_51_49865.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_51_51005.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_51_52373.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_51_53878.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_51_54554.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_51_57508.txtfopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_51_57618.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_51_59484.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_51_6563.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_61_16845.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_61_37106.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_61_37272.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_61_47947.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_61_50754.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_61_55800.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_61_57380.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_65_35328.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_65_36137.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_65_38826.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_65_44596.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_65_51275.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_65_55671.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_72_20155.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_72_30616.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_72_30653.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_72_30988.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_72_31339.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_72_31527.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_72_31631.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_72_36047.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_72_36568.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_72_36636.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_72_37020.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_72_38128.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_72_43952.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_72_45210.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_72_47889.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_72_51064.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_72_51800.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_72_5330.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_72_57508.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_72_58470.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_72_60894.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_20730.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_20753.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_30097.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_30663.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_35365.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_35375.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_35918.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_36010.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_36780.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_36793.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_37845.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_39110.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_39546.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_43936.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_44405.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_44424.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_44683.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_45166.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_46648.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_46986.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_47070.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_47187.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_48435.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_48817.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_49138.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_49460.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_49519.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_49532.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_49829.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_50608.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_54640.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_87_61082.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_90_15727.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_90_20155.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_90_30407.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_90_3525.txt 142: 142: testChEMBfopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: L_Txt() chembl_II_sets/Target_no_93_12377.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_93_1308.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_93_34759.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_93_35447.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_93_42214.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_93_45877.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_93_47082.txt 142: 142: testChEMBL_Txt() chembl_II_sets/Target_no_93_57082.txt 142: 142: testFileSDF_RandomSet(): benchmark/chembl13-10000-random-pairs.sdf 142: ERROR: RDKit could not load input file 142: 142: testFileSDF_RandomSet(): benchmark/chembl13_pairs.smi 142: ERROR: RDKit could not load input file 142: 142: testFileSDF_RandomSet(): benchmark/chembl13_knearest_2.smi 142: ERROR: RDKit could not load input file 142: 142: testFileSDF_RandomSet(): benchmark/chembl13_knearest_10.smi 142: ERROR: RDKit could not load input file 142: 142: testFileSDF_RandomSet(): benchmark/chembl13_knearest_100.smi 142: ERROR: RDKit could not load input file 142: 142: testFileSDF_RandomSet(): benchmark/chembl13_threshold_80.smi 142: ERROR: RDKit could not load input file 142: 142: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 142: ERROR: RDKit could not load input file 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 143: =============================================================================== 143: All tests passed (60 assertions in 5 test cases) 143: 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 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 145: 145: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 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 145: 2: NOREF. Reference data NOT LISTED in test case. 145: 3: res= O=C(Nc1ccccc1[*:1])[*:2],C[*:1].C[C:3]([NH+]1CCCC1)[*:2] 145: 3: NOREF. Reference data NOT LISTED in test case. 145: 4: res= O=C(Nc1ccccc1[*:1])[C:0]([NH+]1CCCC1)[*:2],C[*:1].C[*:2] 145: 4: NOREF. Reference data NOT LISTED in test case. 145: 5: res= O=C(Nc1ccccc1[*:1])[C:0]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].C[*:2] 145: 5: NOREF. Reference data NOT LISTED in test case. 145: 6: res= C[C:0](C(=O)Nc1ccccc1[*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 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. 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] 145: 9: NOREF. Reference data NOT LISTED in test case. 145: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3] 145: 10: NOREF. Reference data NOT LISTED in test case. 145: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2] 145: 11: NOREF. Reference data NOT LISTED in test case. 145: 12: res= NULL,C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1NC(=O)[*:1] 145: 12: NOREF. Reference data NOT LISTED in test case. 145: 13: res= C1CC[NH+]([C:0]([*:1])[*:2])C1,C[*:1].Cc1ccccc1NC(=O)[*:2] 145: 13: NOREF. Reference data NOT LISTED in test case. 145: 14: res= [C:0]([*:1])([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].Cc1ccccc1NC(=O)[*:2] 145: 14: NOREF. Reference data NOT LISTED in test case. 145: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] 145: 15: NOREF. Reference data NOT LISTED in test case. 145: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1] 145: 16: NOREF. Reference data NOT LISTED in test case. 145: 17: res= Cc1ccccc1NC(=O)[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 145: 17: NOREF. Reference data NOT LISTED in test case. 145: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 145: 18: NOREF. Reference data NOT LISTED in test case. 145: 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 0.012167 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 145: 1: PASSED. matchedRefRes = 4 145: 2: O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21, C[*:1].O=C(NCCO)[*:2] 145: 2: PASSED. matchedRefRes = 1 145: 3: O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].OCC[*:2] 145: 3: PASSED. matchedRefRes = 6 145: 4: O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].OC[*:2] 145: 4: PASSED. matchedRefRes = 13 145: 5: O=C(NCC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].O[*:2] 145: 5: PASSED. matchedRefRes = 12 145: 6: NULL, Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O=C(NCCO)[*:1] 145: 6: PASSED. matchedRefRes = 10 145: 7: O=C(N[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 145: 7: NOREF. Reference data NOT LISTED in test case.O=C(N[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 145: 8: O=C(NC[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 145: 8: NOREF. Reference data NOT LISTED in test case.O=C(NC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 145: 9: O=C(NCC[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 145: 9: NOREF. Reference data NOT LISTED in test case.O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 145: 10: NULL, Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 145: 10: PASSED. matchedRefRes = 3 145: 11: C([*:1])[*:2], Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 145: 11: NOREF. Reference data NOT LISTED in test case.C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 145: 12: C(C[*:2])[*:1], Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 145: 12: PASSED. matchedRefRes = 8 145: 13: NULL, Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] 145: 13: PASSED. matchedRefRes = 9 145: 14: C([*:1])[*:2], Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 145: 14: PASSED. matchedRefRes = 11 145: 15: NULL, Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 145: 15: PASSED. matchedRefRes = 2 145: 145: --- UNMATCHED Reference RESULTS: --- 145: 5: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] 145: 7: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(N[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:2] 145: 14: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NCC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 145: 15: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] 145: ----------------------------------- 145: 145: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 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] 145: 2: PASSED. matchedRefRes = 1 145: 3: res= O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OCC[*:2] 145: 3: PASSED. matchedRefRes = 6 145: 4: res= O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OC[*:2] 145: 4: PASSED. matchedRefRes = 13 145: 5: res= O=C(NCC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].O[*:2] 145: 5: PASSED. matchedRefRes = 12 145: 6: res= NULL,Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O=C(NCCO)[*:1] 145: 6: PASSED. matchedRefRes = 10 145: 7: res= O=C(N[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 145: 7: NOREF. Reference data NOT LISTED in test case. 145: 8: res= O=C(NC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 145: 8: NOREF. Reference data NOT LISTED in test case. 145: 9: res= O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 145: 9: NOREF. Reference data NOT LISTED in test case. 145: 10: res= NULL,Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 145: 10: PASSED. matchedRefRes = 3 145: 11: res= C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 145: 11: NOREF. Reference data NOT LISTED in test case. 145: 12: res= C(C[*:2])[*:1],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 145: 12: PASSED. matchedRefRes = 8 145: 13: res= NULL,Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] 145: 13: PASSED. matchedRefRes = 9 145: 14: res= C([*:1])[*:2],Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 145: 14: PASSED. matchedRefRes = 11 145: 15: res= NULL,Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 145: 15: PASSED. matchedRefRes = 2 145: 145: --- UNMATCHED Reference RESULTS: --- 145: 5: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] 145: 7: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(N[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:2] 145: 14: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NCC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 145: 15: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,O=C(NC[*:2])[*:1],Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] 145: ----------------------------------- 145: 145: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE 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] 145: 2: PASSED. matchedRefRes = 3 145: 3: res= C([*:1])([*:2])[*:3],C1CN1[*:3].C[*:1].O=C[*:2] 145: 3: NOREF. Reference data NOT LISTED in test case. 145: 4: res= C1CN1C([*:1])[*:2],C[*:1].O=C[*:2] 145: 4: PASSED. matchedRefRes = 4 145: 5: res= NULL,C1CN1[*:1].CC(C=O)[*:1] 145: 5: PASSED. matchedRefRes = 5 145: 6: res= CC([*:1])[*:2],C1CN1[*:2].O=C[*:1] 145: 6: NOREF. Reference data NOT LISTED in test case. 145: 7: res= NULL,CC(N1CC1)[*:1].O=C[*:1] 145: 7: PASSED. matchedRefRes = 7 145: 145: --- UNMATCHED Reference RESULTS: --- 145: 1: CC(N1CC1)C(=O),Case1-SIMPLE,C([*:1])([*:2])[*:3],C1CN1[*:2].C[*:1].O=C[*:3] 145: 6: CC(N1CC1)C(=O),Case1-SIMPLE,CC([*:1])[*:2],C1CN1[*:1].O=C[*:2] 145: ----------------------------------- 145: 145: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 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 145: 2: NOREF. Reference data NOT LISTED in test case. 145: 3: res= O=C(Nc1ccccc1[*:1])[*:2],C[*:1].C[C:3]([NH+]1CCCC1)[*:2] 145: 3: NOREF. Reference data NOT LISTED in test case. 145: 4: res= O=C(Nc1ccccc1[*:1])[C:0]([NH+]1CCCC1)[*:2],C[*:1].C[*:2] 145: 4: NOREF. Reference data NOT LISTED in test case. 145: 5: res= O=C(Nc1ccccc1[*:1])[C:0]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].C[*:2] 145: 5: NOREF. Reference data NOT LISTED in test case. 145: 6: res= C[C:0](C(=O)Nc1ccccc1[*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 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. 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] 145: 9: NOREF. Reference data NOT LISTED in test case. 145: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3] 145: 10: NOREF. Reference data NOT LISTED in test case. 145: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2] 145: 11: NOREF. Reference data NOT LISTED in test case. 145: 12: res= NULL,C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1NC(=O)[*:1] 145: 12: NOREF. Reference data NOT LISTED in test case. 145: 13: res= C1CC[NH+]([C:0]([*:1])[*:2])C1,C[*:1].Cc1ccccc1NC(=O)[*:2] 145: 13: NOREF. Reference data NOT LISTED in test case. 145: 14: res= [C:0]([*:1])([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].Cc1ccccc1NC(=O)[*:2] 145: 14: NOREF. Reference data NOT LISTED in test case. 145: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] 145: 15: NOREF. Reference data NOT LISTED in test case. 145: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1] 145: 16: NOREF. Reference data NOT LISTED in test case. 145: 17: res= Cc1ccccc1NC(=O)[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 145: 17: NOREF. Reference data NOT LISTED in test case. 145: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 145: 18: NOREF. Reference data NOT LISTED in test case. 145: 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: 145: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 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 145: 2: NOREF. Reference data NOT LISTED in test case. 145: 3: res= O=C(O[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc(C[*:2])cc1 145: 3: NOREF. Reference data NOT LISTED in test case. 145: 4: res= O=C(O[*:1])C(c1ccccc1)[*:2],O[*:2].c1ccc(C[*:1])cc1 145: 4: NOREF. Reference data NOT LISTED in test case. 145: 5: res= O=C(O[*:1])C([*:2])[*:3],O[*:2].c1ccc(C[*:1])cc1.c1ccc([*:3])cc1 145: 5: NOREF. Reference data NOT LISTED in test case. 145: 6: res= O=C(O[*:1])C(O)[*:2],c1ccc(C[*:1])cc1.c1ccc([*:2])cc1 145: 6: NOREF. Reference data NOT LISTED in test case. 145: 7: res= NULL,O=C(OC[*:1])C(O)c1ccccc1.c1ccc([*:1])cc1 145: 7: NOREF. Reference data NOT LISTED in test case. 145: 8: res= O=C(OC[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc([*:2])cc1 145: 8: NOREF. Reference data NOT LISTED in test case. 145: 9: res= O=C(OC[*:2])C(c1ccccc1)[*:1],O[*:1].c1ccc([*:2])cc1 145: 9: NOREF. Reference data NOT LISTED in test case. 145: 10: res= O=C(OC[*:2])C([*:1])[*:3],O[*:1].c1ccc([*:2])cc1.c1ccc([*:3])cc1 145: 10: NOREF. Reference data NOT LISTED in test case. 145: 11: res= O=C(OC[*:1])C(O)[*:2],c1ccc([*:1])cc1.c1ccc([*:2])cc1 145: 11: NOREF. Reference data NOT LISTED in test case. 145: 12: res= NULL,O=C(OCc1ccccc1)[*:1].OC(c1ccccc1)[*:1] 145: 12: NOREF. Reference data NOT LISTED in test case. 145: 13: res= c1ccc(C([*:1])[*:2])cc1,O=C(OCc1ccccc1)[*:1].O[*:2] 145: 13: NOREF. Reference data NOT LISTED in test case. 145: 14: res= C([*:1])([*:2])[*:3],O=C(OCc1ccccc1)[*:1].O[*:2].c1ccc([*:3])cc1 145: 14: PASSED. matchedRefRes = 1 145: 15: res= OC([*:1])[*:2],O=C(OCc1ccccc1)[*:1].c1ccc([*:2])cc1 145: 15: NOREF. Reference data NOT LISTED in test case. 145: 16: res= NULL,O=C(OCc1ccccc1)C(c1ccccc1)[*:1].O[*:1] 145: 16: NOREF. Reference data NOT LISTED in test case. 145: 17: res= O=C(OCc1ccccc1)C([*:1])[*:2],O[*:1].c1ccc([*:2])cc1 145: 17: NOREF. Reference data NOT LISTED in test case. 145: 18: res= NULL,O=C(OCc1ccccc1)C(O)[*:1].c1ccc([*:1])cc1 145: 18: NOREF. Reference data NOT LISTED in test case. 145: 145: --- ALL PASSED --- 145: ----------------------------------- 145: 5 TEST CASES FAILED 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 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: 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 129: ............[16:03:41] Molecule does not have explicit Hs. Consider calling AddHs() 148: ... 148: ---------------------------------------------------------------------- 148: Ran 3 tests in 0.016s 148: 148: OK 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 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 150: =============================================================================== 150: All tests passed (111 assertions in 3 test cases) 150: 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 151: ..... 151: ---------------------------------------------------------------------- 151: Ran 5 tests in 0.058s 151: 151: OK 151: Testing tert-butyldimethylsilyl 151: Testing methoxytrityl 151: Testing tetrahydropyranyl 151: Testing methoxymethyl_ether 151: Testing beta-Methoxyethoxymethyl_ether 151: Testing benzyl 151: Testing trimethylsilyl 151: Testing benzoyl 151: Testing pivaloyl 151: Testing triisopropylsilyl 151: Testing acetyl 151: Testing para-methoxybenzyl_ether 151: Testing triphenylmethyl 151: Testing phthaloyl 151: Testing trimethylsilylethoxymethyl 151: Testing para-methoxyphenyl 151: Testing tosyl 151: Testing tert-butyloxycarbonyl 151: Testing trifluoroacetyl 151: Testing benzoyl 151: Testing 9-fluorenylmethyloxycarbonyl 151: Testing benzylamine 151: Testing acetamide 151: Testing carbobenzyloxy 151: Testing Acetal/Ketal 151: Testing tert-butyldimethylsilyl 151: Testing methoxytrityl 151: Testing tetrahydropyranyl 151: Testing methoxymethyl_ether 151: Testing beta-Methoxyethoxymethyl_ether 151: Testing benzyl 151: Testing trimethylsilyl 151: Testing benzoyl 151: Testing pivaloyl 151: Testing triisopropylsilyl 151: Testing acetyl 151: Testing para-methoxybenzyl_ether 151: Testing triphenylmethyl 151: Testing phthaloyl 151: Testing trimethylsilylethoxymethyl 151: Testing para-methoxyphenyl 151: Testing tosyl 151: Testing tert-butyloxycarbonyl 151: Testing trifluoroacetyl 151: Testing benzoyl 151: Testing 9-fluorenylmethyloxycarbonyl 151: Testing benzylamine 151: Testing acetamide 151: Testing carbobenzyloxy 151: Testing Acetal/Ketal 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, 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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 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: [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 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 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 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 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 160: =============================================================================== 160: All tests passed (142 assertions in 10 test cases) 160: 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 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 162: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 162: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange 162: Test timeout computed to be: 1500 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":"mol1 name","atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"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":[{"name":"test mol","atoms":[{"z":9},{"stereo":"cw"},{"z":17},{"z":8,"impHs":1},{"impHs":3}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[1,4]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2022.09.3","cipRanks":[3,1,4,2,0],"cipCodes":[[1,"S"]]}]}]} 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":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1}],"bonds":[{"bo":2,"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"bo":2,"atoms":[4,5]},{"atoms":[5,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2022.09.3","aromaticAtoms":[0,1,2,3,4,5],"aromaticBonds":[0,1,2,3,4,5],"cipRanks":[0,0,0,0,0,0],"atomRings":[[0,5,4,3,2,1]]}]}]} 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":3},{"impHs":2},{},{},{"z":7,"impHs":2},{"impHs":1},{},{"impHs":3},{"z":7},{"impHs":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[3,5]},{"bo":2,"atoms":[5,6]},{"atoms":[6,7]},{"atoms":[6,8]},{"bo":2,"atoms":[8,9]},{"atoms":[9,2]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2022.09.3","aromaticAtoms":[2,3,5,6,8,9],"aromaticBonds":[2,4,5,7,8,9],"cipRanks":[0,2,4,5,8,3,7,1,9,6],"atomRings":[[2,9,8,6,5,3]]}]}]} 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":"example 2","atoms":[{"z":8},{"stereo":"cw"},{"z":17,"isotope":35},{"z":9},{"z":1},{"z":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[0,4]},{"atoms":[1,5]}],"conformers":[{"dim":2,"coords":[[-1.1987,-0.0452],[-0.3332,0.4555],[0.1659,1.322],[0.5332,-0.0438],[-2.0652,0.4541],[-0.8339,1.3212]]},{"dim":3,"coords":[[0.9553,-0.3743,-0.4679],[-0.3616,-0.131,-0.0794],[-0.5097,1.6255,0.1705],[-0.5778,-0.7919,1.1042],[1.5276,0.1063,0.1627],[-1.0339,-0.4345,-0.8902]]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2022.09.3","cipCodes":[[1,"S"]]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2022.09.3","values":[-0.352,0.273,-0.055,-0.198,0.215,0.117]}]}]} 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]]}]}]} 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: [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: 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 164: . 164: ---------------------------------------------------------------------- 164: Ran 1 test in 0.033s 164: 164: OK 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: [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 0.016s 166: 166: OK 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 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: ............[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: ..[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 167: idx 167: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp 167: Failed Expression: 12 < 6 167: **** 167: 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 167: idx 167: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp 167: Failed Expression: 12 < 6 167: **** 167: 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 168: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/testConformer.py" 168: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/Wrap 168: Test timeout computed to be: 1500 168: ...... 168: ---------------------------------------------------------------------- 168: Ran 6 tests in 0.018s 168: 168: OK 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 158: [16:04:03] Relabelling existing label 169: [16:04:03] 169: 169: **** 169: Pre-condition Violation 169: from must be < size() 169: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 169: Failed Expression: from < static_cast(size()) 169: **** 169: 169: .[16:04:03] 169: 169: **** 169: Pre-condition Violation 169: from must be < size() 169: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 169: Failed Expression: from < static_cast(size()) 169: **** 169: 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 169: snapshotNum 169: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 169: Failed Expression: 0 < 0 169: **** 169: 169: .[16:04:03] 169: 169: **** 169: Pre-condition Violation 169: The trajectory must have dimension == 3 169: Violation occurred on line 113 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 169: Failed Expression: traj.dimension() == 3 169: **** 169: 169: ..[16:04:03] 169: 169: **** 169: Pre-condition Violation 169: The trajectory must have dimension == 3 169: Violation occurred on line 154 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 169: Failed Expression: traj.dimension() == 3 169: **** 169: 169: .[16:04:03] 169: 169: **** 169: Pre-condition Violation 169: d_pos must not be NULL 169: Violation occurred on line 23 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 169: Failed Expression: d_pos 169: **** 169: 169: [16:04:03] 169: 169: **** 169: Pre-condition Violation 169: d_trajectory must not be NULL 169: Violation occurred on line 24 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 169: Failed Expression: d_trajectory 169: **** 169: 169: .[16:04:03] 169: 169: **** 169: Range Error 169: snapshotNum 169: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 169: Failed Expression: 5 < 5 169: **** 169: 169: [16:04:03] 169: 169: **** 169: Range Error 169: pointNum 169: Violation occurred on line 27 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 169: Failed Expression: 10 < 10 169: **** 169: 169: .[16:04:03] 169: 169: **** 169: Range Error 169: snapshotNum 169: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 169: Failed Expression: 5 < 5 169: **** 169: 169: [16:04:03] 169: 169: **** 169: Pre-condition Violation 169: d_dimension must be == 2 169: Violation occurred on line 25 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 169: Failed Expression: d_trajectory->dimension() == 2 169: **** 169: 169: [16:04:03] 169: 169: **** 169: Pre-condition Violation 169: d_dimension must be == 2 169: Violation occurred on line 25 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 169: Failed Expression: d_trajectory->dimension() == 2 169: **** 169: 169: . 169: ---------------------------------------------------------------------- 169: Ran 9 tests in 0.559s 169: 169: OK 169: Testing Trajectory wrapper 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: [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 0.013s 173: 173: OK 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 168/208 Test #171: pyTestThreads .......................... Passed 0.80 sec test 175 Start 175: molStandardizeTest 175: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest 175: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize 175: Test timeout computed to be: 1500 174: . 174: ---------------------------------------------------------------------- 174: Ran 1 test in 0.012s 174: 174: OK 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 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 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 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 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 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: [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 182: * - * - * - * m1 182: * - * - * - * m2 182: * - * - * - * m1 182: * - * - * - * m2 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: 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 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 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: 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 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 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 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 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: 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: ...............[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 191: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Query/testQuery 191: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/Query 191: Test timeout computed to be: 1500 191: Query 191: Query2 191: Equality 191: Greater 191: GreaterEqual 191: Less 191: LessEqual 191: Open Range 191: Closed Range 191: Float 191: With Tolerance 191: Set 191: And 191: Or 191: XOr 191: pointer and copy foo 191: Set2 185/208 Test #191: testQuery .............................. Passed 0.03 sec test 192 Start 192: testMatCalc 192: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc 192: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc 192: Test timeout computed to be: 1500 192: 1.68022e+08 192: 1.73149e+08 192: 1.05549e+08 192: 7.20603e+07 192: 1.41535e+08 192: 1.08592e+08 192: 1.11334e+08 192: 2.05553e+08 192: 1.54962e+08 192: 8.08231e+07 192: 5.61421e+07 192: 1.28874e+08 192: 1.59011e+08 192: 8.69902e+07 192: 1.31367e+08 192: 2.27389e+08 192: 1.60289e+08 192: 7.79813e+07 192: 1.61001e+08 192: 2.07599e+08 192: 2.24432e+08 192: 1.39725e+08 192: 2.42614e+08 192: 1.77578e+08 192: 1.05908e+08 192: 9.06742e+07 192: 1.8087e+08 192: 1.98182e+08 192: 2.03052e+08 192: 1.7673e+08 192: 9.32798e+07 192: 1.37969e+08 192: 1.83778e+08 192: 2.1228e+08 192: 5.06157e+07 192: 1.566e+08 192: 2.37142e+08 192: 1.49345e+08 192: 7.05819e+07 192: 1.71633e+08 192: 1.96817e+08 192: 2.18246e+08 192: 9.49496e+07 192: 2.25618e+08 192: 1.30219e+08 186/208 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 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 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 195: Test command: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers/pickersTestsCatch 195: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/Code/SimDivPickers 195: Test timeout computed to be: 1500 195: =============================================================================== 195: All tests passed (21267 assertions in 1 test case) 195: 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 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 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: [16:04:11] 197: 197: **** 197: Invariant Violation 197: Can't rank more bits than the ensemble size 197: Violation occurred on line 156 in file ./Code/ML/InfoTheory/InfoBitRanker.cpp 197: Failed Expression: num <= dp_maskBits->getNumOnBits() 197: **** 197: 197: ... 197: ---------------------------------------------------------------------- 197: Ran 5 tests in 0.052s 197: 197: OK 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 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: 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 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 200: [16:04:12] INFO: Reading molecules and constructing molecular database. 200: 200: [16:04:12] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: 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: ====================================================================== 202: ERROR: test1_basics (__main__.TestCase.test1_basics) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestBuildComposite.py", line 87, in test1_basics 202: compos = BuildComposite.RunIt(self.details, saveIt=0) 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 752, in RunIt 202: composite = RunOnData(details, data, progressCallback=progressCallback, saveIt=saveIt, 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 403, in RunOnData 202: trainIdx, testIdx = SplitData.SplitIndices( 202: ^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices 202: random.shuffle(perm, random=random.random) 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ====================================================================== 202: ERROR: test2_depth_limit (__main__.TestCase.test2_depth_limit) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestBuildComposite.py", line 109, in test2_depth_limit 202: compos = BuildComposite.RunIt(self.details, saveIt=0) 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 752, in RunIt 202: composite = RunOnData(details, data, progressCallback=progressCallback, saveIt=saveIt, 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 403, in RunOnData 202: trainIdx, testIdx = SplitData.SplitIndices( 202: ^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices 202: random.shuffle(perm, random=random.random) 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ====================================================================== 202: ERROR: test3_depth_limit_less_greedy (__main__.TestCase.test3_depth_limit_less_greedy) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestBuildComposite.py", line 128, in test3_depth_limit_less_greedy 202: compos = BuildComposite.RunIt(self.details, saveIt=0) 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 752, in RunIt 202: composite = RunOnData(details, data, progressCallback=progressCallback, saveIt=saveIt, 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 403, in RunOnData 202: trainIdx, testIdx = SplitData.SplitIndices( 202: ^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices 202: random.shuffle(perm, random=random.random) 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ====================================================================== 202: ERROR: test4_more_trees (__main__.TestCase.test4_more_trees) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestBuildComposite.py", line 147, in test4_more_trees 202: compos = BuildComposite.RunIt(self.details, saveIt=0) 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 752, in RunIt 202: composite = RunOnData(details, data, progressCallback=progressCallback, saveIt=saveIt, 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 403, in RunOnData 202: trainIdx, testIdx = SplitData.SplitIndices( 202: ^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices 202: random.shuffle(perm, random=random.random) 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ====================================================================== 202: ERROR: test5_auto_bounds (__main__.TestCase.test5_auto_bounds) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestBuildComposite.py", line 166, in test5_auto_bounds 202: compos = BuildComposite.RunIt(self.details, saveIt=0) 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 752, in RunIt 202: composite = RunOnData(details, data, progressCallback=progressCallback, saveIt=saveIt, 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 403, in RunOnData 202: trainIdx, testIdx = SplitData.SplitIndices( 202: ^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices 202: random.shuffle(perm, random=random.random) 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ====================================================================== 202: ERROR: test6_auto_bounds_real_activity (__main__.TestCase.test6_auto_bounds_real_activity) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestBuildComposite.py", line 186, in test6_auto_bounds_real_activity 202: compos = BuildComposite.RunIt(self.details, saveIt=0) 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 752, in RunIt 202: composite = RunOnData(details, data, progressCallback=progressCallback, saveIt=saveIt, 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 403, in RunOnData 202: trainIdx, testIdx = SplitData.SplitIndices( 202: ^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices 202: random.shuffle(perm, random=random.random) 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ====================================================================== 202: ERROR: test7_composite_naiveBayes (__main__.TestCase.test7_composite_naiveBayes) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestBuildComposite.py", line 204, in test7_composite_naiveBayes 202: compos = BuildComposite.RunIt(self.details, saveIt=0) 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 752, in RunIt 202: composite = RunOnData(details, data, progressCallback=progressCallback, saveIt=saveIt, 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 403, in RunOnData 202: trainIdx, testIdx = SplitData.SplitIndices( 202: ^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices 202: random.shuffle(perm, random=random.random) 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- 202: Ran 7 tests in 0.151s 202: 202: FAILED (errors=7) 203: ....... 203: ---------------------------------------------------------------------- 203: Ran 7 tests in 0.045s 203: 203: OK 200: [16:04:13] INFO: Reading molecules and constructing molecular database. 200: 200: [16:04:13] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: 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) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestScreenComposite.py", line 282, in test10_filtering 202: nGood, misCount, nSkipped, avgGood, avgBad, avgSkip, tbl = ScreenComposite.ScreenFromDetails( 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/ScreenComposite.py", line 722, in ScreenFromDetails 202: nGood = numpy.zeros(nModels, numpy.float) 202: ^^^^^^^^^^^ 202: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ 202: raise AttributeError(__former_attrs__[attr]) 202: AttributeError: module 'numpy' has no attribute 'float'. 202: `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. 202: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 202: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 202: 202: ====================================================================== 202: ERROR: test11_filtering_segmentation (__main__.TestCase.test11_filtering_segmentation) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestScreenComposite.py", line 309, in test11_filtering_segmentation 202: nGood, misCount, nSkipped, avgGood, avgBad, avgSkip, tbl = ScreenComposite.ScreenFromDetails( 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/ScreenComposite.py", line 722, in ScreenFromDetails 202: nGood = numpy.zeros(nModels, numpy.float) 202: ^^^^^^^^^^^ 202: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ 202: raise AttributeError(__former_attrs__[attr]) 202: AttributeError: module 'numpy' has no attribute 'float'. 202: `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. 202: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 202: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 202: 202: ====================================================================== 202: ERROR: test12_naiveBayes_composite (__main__.TestCase.test12_naiveBayes_composite) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestScreenComposite.py", line 334, in test12_naiveBayes_composite 202: nGood, misCount, nSkipped, avgGood, avgBad, avgSkip, tbl = ScreenComposite.ScreenFromDetails( 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/ScreenComposite.py", line 722, in ScreenFromDetails 202: nGood = numpy.zeros(nModels, numpy.float) 202: ^^^^^^^^^^^ 202: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ 202: raise AttributeError(__former_attrs__[attr]) 202: AttributeError: module 'numpy' has no attribute 'float'. 202: `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. 202: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 202: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 202: 202: ====================================================================== 202: ERROR: test1_basics (__main__.TestCase.test1_basics) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestScreenComposite.py", line 44, in test1_basics 202: nGood, misCount, nSkipped, avgGood, avgBad, avgSkip, tbl = ScreenComposite.ScreenFromDetails( 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/ScreenComposite.py", line 722, in ScreenFromDetails 202: nGood = numpy.zeros(nModels, numpy.float) 202: ^^^^^^^^^^^ 202: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ 202: raise AttributeError(__former_attrs__[attr]) 202: AttributeError: module 'numpy' has no attribute 'float'. 202: `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. 202: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 202: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 202: 202: ====================================================================== 202: ERROR: test2_include_holdout (__main__.TestCase.test2_include_holdout) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestScreenComposite.py", line 71, in test2_include_holdout 202: nGood, misCount, nSkipped, avgGood, avgBad, avgSkip, tbl = ScreenComposite.ScreenFromDetails( 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/ScreenComposite.py", line 722, in ScreenFromDetails 202: nGood = numpy.zeros(nModels, numpy.float) 202: ^^^^^^^^^^^ 202: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ 202: raise AttributeError(__former_attrs__[attr]) 202: AttributeError: module 'numpy' has no attribute 'float'. 202: `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. 202: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 202: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 202: 202: ====================================================================== 202: ERROR: test3_include_training (__main__.TestCase.test3_include_training) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestScreenComposite.py", line 98, in test3_include_training 202: nGood, misCount, nSkipped, avgGood, avgBad, avgSkip, tbl = ScreenComposite.ScreenFromDetails( 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/ScreenComposite.py", line 722, in ScreenFromDetails 202: nGood = numpy.zeros(nModels, numpy.float) 202: ^^^^^^^^^^^ 202: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ 202: raise AttributeError(__former_attrs__[attr]) 202: AttributeError: module 'numpy' has no attribute 'float'. 202: `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. 202: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 202: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 202: 202: ====================================================================== 202: ERROR: test4_thresholding (__main__.TestCase.test4_thresholding) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestScreenComposite.py", line 126, in test4_thresholding 202: nGood, misCount, nSkipped, avgGood, avgBad, avgSkip, tbl = ScreenComposite.ScreenFromDetails( 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/ScreenComposite.py", line 722, in ScreenFromDetails 202: nGood = numpy.zeros(nModels, numpy.float) 202: ^^^^^^^^^^^ 202: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ 202: raise AttributeError(__former_attrs__[attr]) 202: AttributeError: module 'numpy' has no attribute 'float'. 202: `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. 202: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 202: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 202: 202: ====================================================================== 202: ERROR: test5_basics (__main__.TestCase.test5_basics) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestScreenComposite.py", line 151, in test5_basics 202: tpl = ScreenComposite.ScreenFromDetails(compos, self.details) 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/ScreenComposite.py", line 722, in ScreenFromDetails 202: nGood = numpy.zeros(nModels, numpy.float) 202: ^^^^^^^^^^^ 202: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ 202: raise AttributeError(__former_attrs__[attr]) 202: AttributeError: module 'numpy' has no attribute 'float'. 202: `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. 202: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 202: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 202: 202: ====================================================================== 202: ERROR: test6_multiple_models (__main__.TestCase.test6_multiple_models) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestScreenComposite.py", line 176, in test6_multiple_models 202: tpl = ScreenComposite.ScreenFromDetails(composites, self.details) 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/ScreenComposite.py", line 722, in ScreenFromDetails 202: nGood = numpy.zeros(nModels, numpy.float) 202: ^^^^^^^^^^^ 202: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ 202: raise AttributeError(__former_attrs__[attr]) 202: AttributeError: module 'numpy' has no attribute 'float'. 202: `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. 202: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 202: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 202: 202: ====================================================================== 202: ERROR: test7_shuffle (__main__.TestCase.test7_shuffle) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestScreenComposite.py", line 206, in test7_shuffle 202: nGood, misCount, nSkipped, avgGood, avgBad, avgSkip, tbl = ScreenComposite.ScreenFromDetails( 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/ScreenComposite.py", line 722, in ScreenFromDetails 202: nGood = numpy.zeros(nModels, numpy.float) 202: ^^^^^^^^^^^ 202: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ 202: raise AttributeError(__former_attrs__[attr]) 202: AttributeError: module 'numpy' has no attribute 'float'. 202: `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. 202: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 202: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 202: 202: ====================================================================== 202: ERROR: test8_shuffle_segmentation (__main__.TestCase.test8_shuffle_segmentation) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestScreenComposite.py", line 231, in test8_shuffle_segmentation 202: nGood, misCount, nSkipped, avgGood, avgBad, avgSkip, tbl = ScreenComposite.ScreenFromDetails( 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/ScreenComposite.py", line 722, in ScreenFromDetails 202: nGood = numpy.zeros(nModels, numpy.float) 202: ^^^^^^^^^^^ 202: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ 202: raise AttributeError(__former_attrs__[attr]) 202: AttributeError: module 'numpy' has no attribute 'float'. 202: `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. 202: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 202: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 202: 202: ====================================================================== 202: ERROR: test9_shuffle_segmentation2 (__main__.TestCase.test9_shuffle_segmentation2) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestScreenComposite.py", line 256, in test9_shuffle_segmentation2 202: nGood, misCount, nSkipped, avgGood, avgBad, avgSkip, tbl = ScreenComposite.ScreenFromDetails( 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/ScreenComposite.py", line 722, in ScreenFromDetails 202: nGood = numpy.zeros(nModels, numpy.float) 202: ^^^^^^^^^^^ 202: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ 202: raise AttributeError(__former_attrs__[attr]) 202: AttributeError: module 'numpy' has no attribute 'float'. 202: `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. 202: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 202: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 202: 202: ---------------------------------------------------------------------- 202: Ran 12 tests in 0.117s 202: 202: FAILED (errors=12) 202: Traceback (most recent call last): 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: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/AnalyzeComposite.py", line 68, in ProcessIt 202: v = res.get(descId, numpy.zeros(nToConsider, numpy.float)) 202: ^^^^^^^^^^^ 202: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ 202: raise AttributeError(__former_attrs__[attr]) 202: AttributeError: module 'numpy' has no attribute 'float'. 202: `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. 202: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 202: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 202: F 202: ====================================================================== 202: FAIL: test1_Issue163 (__main__.TestCase.test1_Issue163) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestAnalyzeComposite.py", line 51, in test1_Issue163 202: self.assertTrue(ok) 202: AssertionError: 0 is not true 202: 202: ---------------------------------------------------------------------- 202: Ran 1 test in 0.040s 202: 202: FAILED (failures=1) 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 0.130s 203: 203: OK 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 0.002s 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 203: ....... 203: ---------------------------------------------------------------------- 203: Ran 7 tests in 0.002s 203: 203: OK 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 4 tests in 0.178s 202: 202: OK 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 13 tests in 0.011s 206: 206: OK 202: E.EEE 202: ====================================================================== 202: ERROR: test1_basics (__main__.TestCase.test1_basics) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/UnitTestFilter.py", line 27, in test1_basics 202: k, r = DataUtils.FilterData(self.d1, 1, frac) 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/DataUtils.py", line 573, in FilterData 202: othersTake = permutation(nOthers) 202: ^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/DataUtils.py", line 68, in permutation 202: random.shuffle(res, random=random.random) 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ====================================================================== 202: ERROR: test3_indicesOnly (__main__.TestCase.test3_indicesOnly) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/UnitTestFilter.py", line 48, in test3_indicesOnly 202: k, r = DataUtils.FilterData(self.d1, 1, frac, indicesOnly=1) 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/DataUtils.py", line 573, in FilterData 202: othersTake = permutation(nOthers) 202: ^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/DataUtils.py", line 68, in permutation 202: random.shuffle(res, random=random.random) 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ====================================================================== 202: ERROR: test4_indicesOnly_indicesToUse (__main__.TestCase.test4_indicesOnly_indicesToUse) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/UnitTestFilter.py", line 71, in test4_indicesOnly_indicesToUse 202: k, r = DataUtils.FilterData(self.d1, 1, frac, indicesToUse=range(nPts), indicesOnly=1) 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/DataUtils.py", line 573, in FilterData 202: othersTake = permutation(nOthers) 202: ^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/DataUtils.py", line 68, in permutation 202: random.shuffle(res, random=random.random) 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ====================================================================== 202: ERROR: test5_indicesToUse (__main__.TestCase.test5_indicesToUse) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/UnitTestFilter.py", line 94, in test5_indicesToUse 202: k, r = DataUtils.FilterData(self.d1, 1, frac, indicesToUse=range(nPts)) 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/DataUtils.py", line 573, in FilterData 202: othersTake = permutation(nOthers) 202: ^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/DataUtils.py", line 68, in permutation 202: random.shuffle(res, random=random.random) 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- 202: Ran 5 tests in 0.004s 202: 202: FAILED (errors=4) 204: . 204: ---------------------------------------------------------------------- 204: Ran 1 test in 0.001s 204: 204: OK 202: .......E. 202: ====================================================================== 202: ERROR: test_RandomizeActivities (__main__.TestCase.test_RandomizeActivities) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/UnitTestMLData.py", line 139, in test_RandomizeActivities 202: DataUtils.RandomizeActivities(dataSet, shuffle=True, runDetails=details) 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/DataUtils.py", line 655, in RandomizeActivities 202: random.shuffle(acts, random=random.random) 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- 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 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 0.028s 202: 202: OK 202: ********************************************************************** 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 208, in __main__.SplitDbData 202: Failed example: 202: train,test = SplitDbData(conn,1./3.,'basic_2class') 202: Exception raised: 202: Traceback (most recent call last): 202: File "/usr/lib/python3.11/doctest.py", line 1351, in __run 202: exec(compile(example.source, filename, "single", 202: File "", line 1, in 202: train,test = SplitDbData(conn,1./3.,'basic_2class') 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 261, in SplitDbData 202: train, test = SplitIndices(nRes, frac, silent=1) 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices 202: random.shuffle(perm, random=random.random) 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: ********************************************************************** 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 209, in __main__.SplitDbData 202: Failed example: 202: [str(x) for x in train] 202: Exception raised: 202: Traceback (most recent call last): 202: File "/usr/lib/python3.11/doctest.py", line 1351, in __run 202: exec(compile(example.source, filename, "single", 202: File "", line 1, in 202: [str(x) for x in train] 202: ^^^^^ 202: NameError: name 'train' is not defined 202: ********************************************************************** 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 214, in __main__.SplitDbData 202: Failed example: 202: train,test = SplitDbData(conn,.5,'basic_2class',useActs=1) 202: Exception raised: 202: Traceback (most recent call last): 202: File "/usr/lib/python3.11/doctest.py", line 1351, in __run 202: exec(compile(example.source, filename, "single", 202: File "", line 1, in 202: train,test = SplitDbData(conn,.5,'basic_2class',useActs=1) 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 289, in SplitDbData 202: train, test = SplitIndices(nRes, frac, silent=1) 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices 202: random.shuffle(perm, random=random.random) 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: ********************************************************************** 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 215, in __main__.SplitDbData 202: Failed example: 202: [str(x) for x in train] 202: Exception raised: 202: Traceback (most recent call last): 202: File "/usr/lib/python3.11/doctest.py", line 1351, in __run 202: exec(compile(example.source, filename, "single", 202: File "", line 1, in 202: [str(x) for x in train] 202: ^^^^^ 202: NameError: name 'train' is not defined 202: ********************************************************************** 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 223, in __main__.SplitDbData 202: Failed example: 202: train,test = SplitDbData(conn,[.5,1./3.],'basic_2class',useActs=1) 202: Exception raised: 202: Traceback (most recent call last): 202: File "/usr/lib/python3.11/doctest.py", line 1351, in __run 202: exec(compile(example.source, filename, "single", 202: File "", line 1, in 202: train,test = SplitDbData(conn,[.5,1./3.],'basic_2class',useActs=1) 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 289, in SplitDbData 202: train, test = SplitIndices(nRes, frac, silent=1) 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices 202: random.shuffle(perm, random=random.random) 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: ********************************************************************** 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 224, in __main__.SplitDbData 202: Failed example: 202: [str(x) for x in train] 202: Exception raised: 202: Traceback (most recent call last): 202: File "/usr/lib/python3.11/doctest.py", line 1351, in __run 202: exec(compile(example.source, filename, "single", 202: File "", line 1, in 202: [str(x) for x in train] 202: ^^^^^ 202: NameError: name 'train' is not defined 202: ********************************************************************** 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 230, in __main__.SplitDbData 202: Failed example: 202: train,test = SplitDbData(conn,.5,'float_2class',useActs=1,actBounds=[1.0]) 202: Exception raised: 202: Traceback (most recent call last): 202: File "/usr/lib/python3.11/doctest.py", line 1351, in __run 202: exec(compile(example.source, filename, "single", 202: File "", line 1, in 202: train,test = SplitDbData(conn,.5,'float_2class',useActs=1,actBounds=[1.0]) 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 289, in SplitDbData 202: train, test = SplitIndices(nRes, frac, silent=1) 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices 202: random.shuffle(perm, random=random.random) 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: ********************************************************************** 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 231, in __main__.SplitDbData 202: Failed example: 202: [str(x) for x in train] 202: Exception raised: 202: Traceback (most recent call last): 202: File "/usr/lib/python3.11/doctest.py", line 1351, in __run 202: exec(compile(example.source, filename, "single", 202: File "", line 1, in 202: [str(x) for x in train] 202: ^^^^^ 202: NameError: name 'train' is not defined 202: ********************************************************************** 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 54, in __main__.SplitIndices 202: Failed example: 202: test,train = SplitIndices(10,.5) 202: Exception raised: 202: Traceback (most recent call last): 202: File "/usr/lib/python3.11/doctest.py", line 1351, in __run 202: exec(compile(example.source, filename, "single", 202: File "", line 1, in 202: test,train = SplitIndices(10,.5) 202: ^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices 202: random.shuffle(perm, random=random.random) 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: ********************************************************************** 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 55, in __main__.SplitIndices 202: Failed example: 202: test 202: Exception raised: 202: Traceback (most recent call last): 202: File "/usr/lib/python3.11/doctest.py", line 1351, in __run 202: exec(compile(example.source, filename, "single", 202: File "", line 1, in 202: test 202: NameError: name 'test' is not defined 202: ********************************************************************** 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 57, in __main__.SplitIndices 202: Failed example: 202: train 202: Exception raised: 202: Traceback (most recent call last): 202: File "/usr/lib/python3.11/doctest.py", line 1351, in __run 202: exec(compile(example.source, filename, "single", 202: File "", line 1, in 202: train 202: NameError: name 'train' is not defined 202: ********************************************************************** 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 60, in __main__.SplitIndices 202: Failed example: 202: test,train = SplitIndices(10,.5) 202: Exception raised: 202: Traceback (most recent call last): 202: File "/usr/lib/python3.11/doctest.py", line 1351, in __run 202: exec(compile(example.source, filename, "single", 202: File "", line 1, in 202: test,train = SplitIndices(10,.5) 202: ^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices 202: random.shuffle(perm, random=random.random) 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: ********************************************************************** 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 61, in __main__.SplitIndices 202: Failed example: 202: test 202: Exception raised: 202: Traceback (most recent call last): 202: File "/usr/lib/python3.11/doctest.py", line 1351, in __run 202: exec(compile(example.source, filename, "single", 202: File "", line 1, in 202: test 202: NameError: name 'test' is not defined 202: ********************************************************************** 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 63, in __main__.SplitIndices 202: Failed example: 202: train 202: Exception raised: 202: Traceback (most recent call last): 202: File "/usr/lib/python3.11/doctest.py", line 1351, in __run 202: exec(compile(example.source, filename, "single", 202: File "", line 1, in 202: train 202: NameError: name 'train' is not defined 202: ********************************************************************** 202: 2 items had failures: 202: 8 of 16 in __main__.SplitDbData 202: 6 of 22 in __main__.SplitIndices 202: ***Test Failed*** 14 failures. 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: ...... 208: ---------------------------------------------------------------------- 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 5 tests in 0.017s 208: 208: OK 202: .... 202: ---------------------------------------------------------------------- 202: Ran 4 tests in 0.246s 202: 202: OK 200: [16:04:18] INFO: Finished. 200: 208: .... 208: ---------------------------------------------------------------------- 208: Ran 4 tests in 0.012s 208: 208: OK 202: ...... 202: ---------------------------------------------------------------------- 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 0.128s 202: 202: OK 208: ...................... 208: ---------------------------------------------------------------------- 208: Ran 22 tests in 0.039s 208: 208: OK 202: ........E. 202: ====================================================================== 202: ERROR: test8RandomForest (__main__.TestCase.test8RandomForest) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/DecTree/UnitTestQuantTree.py", line 204, in test8RandomForest 202: self.t1 = BuildQuantTree.QuantTreeBoot(examples, attrs, nPossibleVals, boundsPerVar, maxDepth=1, 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/DecTree/BuildQuantTree.py", line 235, in QuantTreeBoot 202: best, gainHere, qBounds = FindBest(resCodes, examples, nBoundsPerVar, nPossibleRes, 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/DecTree/BuildQuantTree.py", line 34, in FindBest 202: random.shuffle(ids, random=random.random) 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- 202: Ran 10 tests in 0.012s 202: 202: FAILED (errors=1) 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 0.150s 202: 202: OK 202: !!! TEST FAILURE: python UnitTestQuantTree.py {} 202: .. 202: ---------------------------------------------------------------------- 202: Ran 2 tests in 0.004s 202: 202: OK 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) 202: ^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/GraphDescriptors.py", line 124, in Ipc 202: cPoly = abs(Graphs.CharacteristicPolynomial(mol, adjMat)) 202: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/Graphs.py", line 43, in CharacteristicPolynomial 202: res = numpy.zeros(nAtoms + 1, numpy.float) 202: ^^^^^^^^^^^ 202: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ 202: raise AttributeError(__former_attrs__[attr]) 202: AttributeError: module 'numpy' has no attribute 'float'. 202: `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. 202: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 202: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 202: E 202: ====================================================================== 202: ERROR: test_github3511 (__main__.TestDescriptors.test_github3511) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Descriptors/UnitTestMolDescriptors.py", line 95, in test_github3511 202: pickle.dumps(mol) 202: RuntimeError: Incomplete pickle support (__getstate_manages_dict__ not set) 202: 202: ---------------------------------------------------------------------- 202: Ran 5 tests in 0.018s 202: 202: FAILED (errors=1) 202: ... 202: ---------------------------------------------------------------------- 202: Ran 3 tests in 0.012s 202: 202: OK 202: !!! TEST FAILURE: python UnitTestMolDescriptors.py {} 202: EEE 202: ====================================================================== 202: ERROR: test0CorrMat (__main__.TestCase.test0CorrMat) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/InfoTheory/UnitTestCorrMatGen.py", line 48, in setUp 202: random.shuffle(obits, random=random.random) 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ====================================================================== 202: ERROR: test1Cluster (__main__.TestCase.test1Cluster) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/InfoTheory/UnitTestCorrMatGen.py", line 48, in setUp 202: random.shuffle(obits, random=random.random) 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ====================================================================== 202: ERROR: test_getValLTM (__main__.TestCase.test_getValLTM) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/InfoTheory/UnitTestCorrMatGen.py", line 48, in setUp 202: random.shuffle(obits, random=random.random) 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- 202: Ran 3 tests in 0.002s 202: 202: FAILED (errors=3) 202: !!! TEST FAILURE: python UnitTestCorrMatGen.py {} 208: ................................... 208: ---------------------------------------------------------------------- 208: Ran 35 tests in 1.058s 208: 208: OK 202: ...... 202: ---------------------------------------------------------------------- 202: Ran 6 tests in 0.577s 202: 202: OK 208: .... 208: ---------------------------------------------------------------------- 208: Ran 4 tests in 0.028s 208: 208: OK 208: . 208: ---------------------------------------------------------------------- 208: Ran 1 test in 0.018s 208: 208: OK 202: ...EE.. 202: ====================================================================== 202: ERROR: testPerm1 (__main__.TestCase.testPerm1) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/ModelPackage/UnitTestPackage.py", line 101, in testPerm1 202: random.shuffle(perm, random=random.random) 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ====================================================================== 202: ERROR: testPerm2 (__main__.TestCase.testPerm2) 202: ---------------------------------------------------------------------- 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/ModelPackage/UnitTestPackage.py", line 117, in testPerm2 202: random.shuffle(perm, random=random.random) 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- 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 0.016s 202: 202: OK 208: ... 208: ---------------------------------------------------------------------- 208: Ran 3 tests in 0.060s 208: 208: OK 208: .ss.ss....... 208: ---------------------------------------------------------------------- 208: Ran 13 tests in 1.856s 208: 208: OK (skipped=4) 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 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 202: 202: OK 202: .... 202: ---------------------------------------------------------------------- 202: Ran 4 tests in 0.001s 202: 202: OK 202: .... 202: ---------------------------------------------------------------------- 202: Ran 4 tests in 0.005s 202: 202: OK 202: !!! TEST FAILURE: python UnitTestBuildComposite.py {} 202: !!! TEST FAILURE: python UnitTestScreenComposite.py {} 202: !!! TEST FAILURE: python UnitTestAnalyzeComposite.py {} 202: !!! TEST FAILURE: python test_list.py {'dir': 'Data'} 202: !!! TEST FAILURE: python test_list.py {'dir': 'DecTree'} 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'} 204/208 Test #202: pythonTestDirML ........................***Failed 15.01 sec EEEEEEE ====================================================================== ERROR: test1_basics (__main__.TestCase.test1_basics) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestBuildComposite.py", line 87, in test1_basics compos = BuildComposite.RunIt(self.details, saveIt=0) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 752, in RunIt composite = RunOnData(details, data, progressCallback=progressCallback, saveIt=saveIt, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 403, in RunOnData trainIdx, testIdx = SplitData.SplitIndices( ^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices random.shuffle(perm, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ====================================================================== ERROR: test2_depth_limit (__main__.TestCase.test2_depth_limit) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestBuildComposite.py", line 109, in test2_depth_limit compos = BuildComposite.RunIt(self.details, saveIt=0) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 752, in RunIt composite = RunOnData(details, data, progressCallback=progressCallback, saveIt=saveIt, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 403, in RunOnData trainIdx, testIdx = SplitData.SplitIndices( ^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices random.shuffle(perm, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ====================================================================== ERROR: test3_depth_limit_less_greedy (__main__.TestCase.test3_depth_limit_less_greedy) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestBuildComposite.py", line 128, in test3_depth_limit_less_greedy compos = BuildComposite.RunIt(self.details, saveIt=0) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 752, in RunIt composite = RunOnData(details, data, progressCallback=progressCallback, saveIt=saveIt, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 403, in RunOnData trainIdx, testIdx = SplitData.SplitIndices( ^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices random.shuffle(perm, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ====================================================================== ERROR: test4_more_trees (__main__.TestCase.test4_more_trees) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestBuildComposite.py", line 147, in test4_more_trees compos = BuildComposite.RunIt(self.details, saveIt=0) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 752, in RunIt composite = RunOnData(details, data, progressCallback=progressCallback, saveIt=saveIt, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 403, in RunOnData trainIdx, testIdx = SplitData.SplitIndices( ^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices random.shuffle(perm, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ====================================================================== ERROR: test5_auto_bounds (__main__.TestCase.test5_auto_bounds) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestBuildComposite.py", line 166, in test5_auto_bounds compos = BuildComposite.RunIt(self.details, saveIt=0) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 752, in RunIt composite = RunOnData(details, data, progressCallback=progressCallback, saveIt=saveIt, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 403, in RunOnData trainIdx, testIdx = SplitData.SplitIndices( ^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices random.shuffle(perm, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ====================================================================== ERROR: test6_auto_bounds_real_activity (__main__.TestCase.test6_auto_bounds_real_activity) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestBuildComposite.py", line 186, in test6_auto_bounds_real_activity compos = BuildComposite.RunIt(self.details, saveIt=0) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 752, in RunIt composite = RunOnData(details, data, progressCallback=progressCallback, saveIt=saveIt, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 403, in RunOnData trainIdx, testIdx = SplitData.SplitIndices( ^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices random.shuffle(perm, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ====================================================================== ERROR: test7_composite_naiveBayes (__main__.TestCase.test7_composite_naiveBayes) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestBuildComposite.py", line 204, in test7_composite_naiveBayes compos = BuildComposite.RunIt(self.details, saveIt=0) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 752, in RunIt composite = RunOnData(details, data, progressCallback=progressCallback, saveIt=saveIt, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/BuildComposite.py", line 403, in RunOnData trainIdx, testIdx = SplitData.SplitIndices( ^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices random.shuffle(perm, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- Ran 7 tests in 0.151s FAILED (errors=7) EEEEEEEEEEEE ====================================================================== ERROR: test10_filtering (__main__.TestCase.test10_filtering) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestScreenComposite.py", line 282, in test10_filtering nGood, misCount, nSkipped, avgGood, avgBad, avgSkip, tbl = ScreenComposite.ScreenFromDetails( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/ScreenComposite.py", line 722, in ScreenFromDetails nGood = numpy.zeros(nModels, numpy.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: test11_filtering_segmentation (__main__.TestCase.test11_filtering_segmentation) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestScreenComposite.py", line 309, in test11_filtering_segmentation nGood, misCount, nSkipped, avgGood, avgBad, avgSkip, tbl = ScreenComposite.ScreenFromDetails( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/ScreenComposite.py", line 722, in ScreenFromDetails nGood = numpy.zeros(nModels, numpy.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: test12_naiveBayes_composite (__main__.TestCase.test12_naiveBayes_composite) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestScreenComposite.py", line 334, in test12_naiveBayes_composite nGood, misCount, nSkipped, avgGood, avgBad, avgSkip, tbl = ScreenComposite.ScreenFromDetails( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/ScreenComposite.py", line 722, in ScreenFromDetails nGood = numpy.zeros(nModels, numpy.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: test1_basics (__main__.TestCase.test1_basics) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestScreenComposite.py", line 44, in test1_basics nGood, misCount, nSkipped, avgGood, avgBad, avgSkip, tbl = ScreenComposite.ScreenFromDetails( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/ScreenComposite.py", line 722, in ScreenFromDetails nGood = numpy.zeros(nModels, numpy.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: test2_include_holdout (__main__.TestCase.test2_include_holdout) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestScreenComposite.py", line 71, in test2_include_holdout nGood, misCount, nSkipped, avgGood, avgBad, avgSkip, tbl = ScreenComposite.ScreenFromDetails( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/ScreenComposite.py", line 722, in ScreenFromDetails nGood = numpy.zeros(nModels, numpy.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: test3_include_training (__main__.TestCase.test3_include_training) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestScreenComposite.py", line 98, in test3_include_training nGood, misCount, nSkipped, avgGood, avgBad, avgSkip, tbl = ScreenComposite.ScreenFromDetails( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/ScreenComposite.py", line 722, in ScreenFromDetails nGood = numpy.zeros(nModels, numpy.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: test4_thresholding (__main__.TestCase.test4_thresholding) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestScreenComposite.py", line 126, in test4_thresholding nGood, misCount, nSkipped, avgGood, avgBad, avgSkip, tbl = ScreenComposite.ScreenFromDetails( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/ScreenComposite.py", line 722, in ScreenFromDetails nGood = numpy.zeros(nModels, numpy.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: test5_basics (__main__.TestCase.test5_basics) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestScreenComposite.py", line 151, in test5_basics tpl = ScreenComposite.ScreenFromDetails(compos, self.details) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/ScreenComposite.py", line 722, in ScreenFromDetails nGood = numpy.zeros(nModels, numpy.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: test6_multiple_models (__main__.TestCase.test6_multiple_models) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestScreenComposite.py", line 176, in test6_multiple_models tpl = ScreenComposite.ScreenFromDetails(composites, self.details) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/ScreenComposite.py", line 722, in ScreenFromDetails nGood = numpy.zeros(nModels, numpy.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: test7_shuffle (__main__.TestCase.test7_shuffle) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestScreenComposite.py", line 206, in test7_shuffle nGood, misCount, nSkipped, avgGood, avgBad, avgSkip, tbl = ScreenComposite.ScreenFromDetails( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/ScreenComposite.py", line 722, in ScreenFromDetails nGood = numpy.zeros(nModels, numpy.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: test8_shuffle_segmentation (__main__.TestCase.test8_shuffle_segmentation) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestScreenComposite.py", line 231, in test8_shuffle_segmentation nGood, misCount, nSkipped, avgGood, avgBad, avgSkip, tbl = ScreenComposite.ScreenFromDetails( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/ScreenComposite.py", line 722, in ScreenFromDetails nGood = numpy.zeros(nModels, numpy.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: test9_shuffle_segmentation2 (__main__.TestCase.test9_shuffle_segmentation2) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestScreenComposite.py", line 256, in test9_shuffle_segmentation2 nGood, misCount, nSkipped, avgGood, avgBad, avgSkip, tbl = ScreenComposite.ScreenFromDetails( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/ScreenComposite.py", line 722, in ScreenFromDetails nGood = numpy.zeros(nModels, numpy.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 12 tests in 0.117s FAILED (errors=12) Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestAnalyzeComposite.py", line 44, in test1_Issue163 res = sorted(AnalyzeComposite.ProcessIt([c1, c2], verbose=-1)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/AnalyzeComposite.py", line 68, in ProcessIt v = res.get(descId, numpy.zeros(nToConsider, numpy.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 F ====================================================================== FAIL: test1_Issue163 (__main__.TestCase.test1_Issue163) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestAnalyzeComposite.py", line 51, in test1_Issue163 self.assertTrue(ok) AssertionError: 0 is not true ---------------------------------------------------------------------- Ran 1 test in 0.040s FAILED (failures=1) ... ---------------------------------------------------------------------- Ran 3 tests in 0.002s OK ........ ---------------------------------------------------------------------- Ran 8 tests in 0.001s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.178s OK E.EEE ====================================================================== ERROR: test1_basics (__main__.TestCase.test1_basics) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/UnitTestFilter.py", line 27, in test1_basics k, r = DataUtils.FilterData(self.d1, 1, frac) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/DataUtils.py", line 573, in FilterData othersTake = permutation(nOthers) ^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/DataUtils.py", line 68, in permutation random.shuffle(res, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ====================================================================== ERROR: test3_indicesOnly (__main__.TestCase.test3_indicesOnly) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/UnitTestFilter.py", line 48, in test3_indicesOnly k, r = DataUtils.FilterData(self.d1, 1, frac, indicesOnly=1) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/DataUtils.py", line 573, in FilterData othersTake = permutation(nOthers) ^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/DataUtils.py", line 68, in permutation random.shuffle(res, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ====================================================================== ERROR: test4_indicesOnly_indicesToUse (__main__.TestCase.test4_indicesOnly_indicesToUse) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/UnitTestFilter.py", line 71, in test4_indicesOnly_indicesToUse k, r = DataUtils.FilterData(self.d1, 1, frac, indicesToUse=range(nPts), indicesOnly=1) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/DataUtils.py", line 573, in FilterData othersTake = permutation(nOthers) ^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/DataUtils.py", line 68, in permutation random.shuffle(res, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ====================================================================== ERROR: test5_indicesToUse (__main__.TestCase.test5_indicesToUse) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/UnitTestFilter.py", line 94, in test5_indicesToUse k, r = DataUtils.FilterData(self.d1, 1, frac, indicesToUse=range(nPts)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/DataUtils.py", line 573, in FilterData othersTake = permutation(nOthers) ^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/DataUtils.py", line 68, in permutation random.shuffle(res, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- Ran 5 tests in 0.004s FAILED (errors=4) .......E. ====================================================================== ERROR: test_RandomizeActivities (__main__.TestCase.test_RandomizeActivities) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/UnitTestMLData.py", line 139, in test_RandomizeActivities DataUtils.RandomizeActivities(dataSet, shuffle=True, runDetails=details) File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Data/DataUtils.py", line 655, in RandomizeActivities random.shuffle(acts, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- Ran 9 tests in 0.005s FAILED (errors=1) ............ ---------------------------------------------------------------------- Ran 12 tests in 0.003s OK ..... ---------------------------------------------------------------------- Ran 5 tests in 0.028s OK ********************************************************************** File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 208, in __main__.SplitDbData Failed example: train,test = SplitDbData(conn,1./3.,'basic_2class') Exception raised: Traceback (most recent call last): File "/usr/lib/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in train,test = SplitDbData(conn,1./3.,'basic_2class') ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 261, in SplitDbData train, test = SplitIndices(nRes, frac, silent=1) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices random.shuffle(perm, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ********************************************************************** File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 209, in __main__.SplitDbData Failed example: [str(x) for x in train] Exception raised: Traceback (most recent call last): File "/usr/lib/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in [str(x) for x in train] ^^^^^ NameError: name 'train' is not defined ********************************************************************** File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 214, in __main__.SplitDbData Failed example: train,test = SplitDbData(conn,.5,'basic_2class',useActs=1) Exception raised: Traceback (most recent call last): File "/usr/lib/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in train,test = SplitDbData(conn,.5,'basic_2class',useActs=1) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 289, in SplitDbData train, test = SplitIndices(nRes, frac, silent=1) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices random.shuffle(perm, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ********************************************************************** File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 215, in __main__.SplitDbData Failed example: [str(x) for x in train] Exception raised: Traceback (most recent call last): File "/usr/lib/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in [str(x) for x in train] ^^^^^ NameError: name 'train' is not defined ********************************************************************** File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 223, in __main__.SplitDbData Failed example: train,test = SplitDbData(conn,[.5,1./3.],'basic_2class',useActs=1) Exception raised: Traceback (most recent call last): File "/usr/lib/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in train,test = SplitDbData(conn,[.5,1./3.],'basic_2class',useActs=1) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 289, in SplitDbData train, test = SplitIndices(nRes, frac, silent=1) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices random.shuffle(perm, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ********************************************************************** File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 224, in __main__.SplitDbData Failed example: [str(x) for x in train] Exception raised: Traceback (most recent call last): File "/usr/lib/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in [str(x) for x in train] ^^^^^ NameError: name 'train' is not defined ********************************************************************** File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 230, in __main__.SplitDbData Failed example: train,test = SplitDbData(conn,.5,'float_2class',useActs=1,actBounds=[1.0]) Exception raised: Traceback (most recent call last): File "/usr/lib/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in train,test = SplitDbData(conn,.5,'float_2class',useActs=1,actBounds=[1.0]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 289, in SplitDbData train, test = SplitIndices(nRes, frac, silent=1) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices random.shuffle(perm, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ********************************************************************** File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 231, in __main__.SplitDbData Failed example: [str(x) for x in train] Exception raised: Traceback (most recent call last): File "/usr/lib/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in [str(x) for x in train] ^^^^^ NameError: name 'train' is not defined ********************************************************************** File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 54, in __main__.SplitIndices Failed example: test,train = SplitIndices(10,.5) Exception raised: Traceback (most recent call last): File "/usr/lib/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in test,train = SplitIndices(10,.5) ^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices random.shuffle(perm, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ********************************************************************** File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 55, in __main__.SplitIndices Failed example: test Exception raised: Traceback (most recent call last): File "/usr/lib/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in test NameError: name 'test' is not defined ********************************************************************** File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 57, in __main__.SplitIndices Failed example: train Exception raised: Traceback (most recent call last): File "/usr/lib/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in train NameError: name 'train' is not defined ********************************************************************** File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 60, in __main__.SplitIndices Failed example: test,train = SplitIndices(10,.5) Exception raised: Traceback (most recent call last): File "/usr/lib/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in test,train = SplitIndices(10,.5) ^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices random.shuffle(perm, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ********************************************************************** File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 61, in __main__.SplitIndices Failed example: test Exception raised: Traceback (most recent call last): File "/usr/lib/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in test NameError: name 'test' is not defined ********************************************************************** File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 63, in __main__.SplitIndices Failed example: train Exception raised: Traceback (most recent call last): File "/usr/lib/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in train NameError: name 'train' is not defined ********************************************************************** 2 items had failures: 8 of 16 in __main__.SplitDbData 6 of 22 in __main__.SplitIndices ***Test Failed*** 14 failures. !!! TEST FAILURE: python UnitTestFilter.py {} !!! TEST FAILURE: python UnitTestMLData.py {} !!! TEST FAILURE: python SplitData.py {} . ---------------------------------------------------------------------- Ran 1 test in 0.000s OK ...... ---------------------------------------------------------------------- Ran 6 tests in 0.002s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.246s OK ...... ---------------------------------------------------------------------- Ran 6 tests in 0.020s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.128s OK ........E. ====================================================================== ERROR: test8RandomForest (__main__.TestCase.test8RandomForest) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/DecTree/UnitTestQuantTree.py", line 204, in test8RandomForest self.t1 = BuildQuantTree.QuantTreeBoot(examples, attrs, nPossibleVals, boundsPerVar, maxDepth=1, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/DecTree/BuildQuantTree.py", line 235, in QuantTreeBoot best, gainHere, qBounds = FindBest(resCodes, examples, nBoundsPerVar, nPossibleRes, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/DecTree/BuildQuantTree.py", line 34, in FindBest random.shuffle(ids, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- Ran 10 tests in 0.012s FAILED (errors=1) ..... ---------------------------------------------------------------------- Ran 5 tests in 0.150s OK !!! TEST FAILURE: python UnitTestQuantTree.py {} .. ---------------------------------------------------------------------- Ran 2 tests in 0.004s OK ....Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/ML/Descriptors/MoleculeDescriptors.py", line 88, in CalcDescriptors res[i] = fn(mol) ^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/GraphDescriptors.py", line 124, in Ipc cPoly = abs(Graphs.CharacteristicPolynomial(mol, adjMat)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/Graphs.py", line 43, in CharacteristicPolynomial res = numpy.zeros(nAtoms + 1, numpy.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 E ====================================================================== ERROR: test_github3511 (__main__.TestDescriptors.test_github3511) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Descriptors/UnitTestMolDescriptors.py", line 95, in test_github3511 pickle.dumps(mol) RuntimeError: Incomplete pickle support (__getstate_manages_dict__ not set) ---------------------------------------------------------------------- Ran 5 tests in 0.018s FAILED (errors=1) ... ---------------------------------------------------------------------- Ran 3 tests in 0.012s OK !!! TEST FAILURE: python UnitTestMolDescriptors.py {} EEE ====================================================================== ERROR: test0CorrMat (__main__.TestCase.test0CorrMat) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/InfoTheory/UnitTestCorrMatGen.py", line 48, in setUp random.shuffle(obits, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ====================================================================== ERROR: test1Cluster (__main__.TestCase.test1Cluster) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/InfoTheory/UnitTestCorrMatGen.py", line 48, in setUp random.shuffle(obits, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ====================================================================== ERROR: test_getValLTM (__main__.TestCase.test_getValLTM) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/InfoTheory/UnitTestCorrMatGen.py", line 48, in setUp random.shuffle(obits, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- Ran 3 tests in 0.002s FAILED (errors=3) !!! TEST FAILURE: python UnitTestCorrMatGen.py {} ...... ---------------------------------------------------------------------- Ran 6 tests in 0.577s OK ...EE.. ====================================================================== ERROR: testPerm1 (__main__.TestCase.testPerm1) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/ModelPackage/UnitTestPackage.py", line 101, in testPerm1 random.shuffle(perm, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ====================================================================== ERROR: testPerm2 (__main__.TestCase.testPerm2) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/ModelPackage/UnitTestPackage.py", line 117, in testPerm2 random.shuffle(perm, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- Ran 7 tests in 0.102s FAILED (errors=2) !!! TEST FAILURE: python UnitTestPackage.py {} .... ---------------------------------------------------------------------- Ran 4 tests in 0.016s OK ..... ---------------------------------------------------------------------- Ran 5 tests in 3.704s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.002s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.001s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.005s OK !!! TEST FAILURE: python UnitTestBuildComposite.py {} !!! TEST FAILURE: python UnitTestScreenComposite.py {} !!! TEST FAILURE: python UnitTestAnalyzeComposite.py {} !!! TEST FAILURE: python test_list.py {'dir': 'Data'} !!! TEST FAILURE: python test_list.py {'dir': 'DecTree'} !!! TEST FAILURE: python test_list.py {'dir': 'Descriptors'} !!! TEST FAILURE: python test_list.py {'dir': 'InfoTheory'} !!! TEST FAILURE: python test_list.py {'dir': 'ModelPackage'} 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: [16:04:28] INFO: Generating fingerprints and descriptors: 200: 200: [16:04:28] INFO: Finished. 200: 200: [16:04:28] INFO: Reading molecules and constructing molecular database. 200: 200: [16:04:28] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: 200: [16:04:28] INFO: Processing 10 molecules 200: 200: [16:04:28] INFO: Generating fingerprints and descriptors: 200: 200: [16:04:28] INFO: Finished. 200: 200: [16:04:29] INFO: Reading molecules and constructing molecular database. 200: 200: [16:04:29] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: 200: [16:04:29] INFO: Generating fingerprints and descriptors: 200: 200: [16:04:29] INFO: Finished. 200: 200: [16:04:30] INFO: Reading molecules and constructing molecular database. 200: 200: [16:04:30] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: 200: [16:04:30] INFO: Generating fingerprints and descriptors: 200: 200: [16:04:30] INFO: Finished. 200: 200: .[16:04:30] INFO: Guessing that mol format is 'sdf'. Use --molFormat argument if this is wrong. 200: 200: [16:04:30] INFO: Reading molecules and constructing molecular database. 200: 200: [16:04:30] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: 200: [16:04:30] INFO: Processing 163 molecules 200: 200: [16:04:31] INFO: done 100 200: 200: [16:04:31] INFO: Generating fingerprints and descriptors: 200: 200: [16:04:31] INFO: Finished. 200: 200: .[16:04:32] INFO: Reading molecules and constructing molecular database. 200: 200: [16:04:32] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: 200: [16:04:32] INFO: Processing 10 molecules 200: 200: [16:04:32] INFO: Generating fingerprints and descriptors: 200: 200: [16:04:32] INFO: Finished. 200: 200: [16:04:33] INFO: Reading molecules and constructing molecular database. 200: 200: [16:04:33] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: 200: [16:04:33] INFO: Processing 10 molecules 200: 200: [16:04:33] INFO: Generating fingerprints and descriptors: 200: 200: [16:04:33] INFO: Finished. 200: 200: . 200: ---------------------------------------------------------------------- 200: Ran 12 tests in 22.034s 200: 200: OK 205/208 Test #200: pythonTestDbCLI ........................ Passed 22.28 sec 5: [16:04:36] Finished: testMultipleTimes() 5: [16:04:36] 5: ----------------------------------------- 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: [16:05:20] WARNING: More than one matching pattern found - picking one 208: 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) 208: ---------------------------------------------------------------------- 208: Traceback (most recent call last): 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: 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 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'} 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) 208: ---------------------------------------------------------------------- 208: Traceback (most recent call last): 208: File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/UnitTestCatalog.py", line 176, in test7ScoreMolecules 208: scores, obls = BuildFragmentCatalog.ScoreMolecules(suppl, cat, acts=self.list2Acts, 208: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 208: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/BuildFragmentCatalog.py", line 164, in ScoreMolecules 208: resTbl = numpy.zeros((nBits, 2, nActs), numpy.int) 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 'int'. 208: `np.int` was a deprecated alias for the builtin `int`. To avoid this error in existing code, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information. 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 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) 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: FTraceback (most recent call last): 208: File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/UnitTestDescriptors.py", line 44, in testGithub1287 208: _ = fn(m) 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 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) 208: ---------------------------------------------------------------------- 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) 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: During handling of the above exception, another exception occurred: 208: 208: Traceback (most recent call last): 208: File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/UnitTestDescriptors.py", line 64, in testBadAtomHandling 208: raise AssertionError('SMILES: %s; Descriptor: %s' % (smi, nm)) 208: AssertionError: SMILES: CC[Pu]; Descriptor: Ipc 208: 208: ====================================================================== 208: FAIL: testGithub1287 (__main__.TestCase.testGithub1287) 208: ---------------------------------------------------------------------- 208: Traceback (most recent call last): 208: File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/UnitTestDescriptors.py", line 44, in testGithub1287 208: _ = fn(m) 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: During handling of the above exception, another exception occurred: 208: 208: Traceback (most recent call last): 208: File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/UnitTestDescriptors.py", line 48, in testGithub1287 208: raise AssertionError('SMILES: %s; Descriptor: %s' % (smi, nm)) 208: AssertionError: SMILES: CCC; Descriptor: Ipc 208: 208: ---------------------------------------------------------------------- 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 1.500s 208: 208: OK 208: ...... 208: ---------------------------------------------------------------------- 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 2.593s 208: 208: OK (skipped=2) 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: [16:05:49] WARNING: More than one matching pattern found - picking one 208: 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) 208: Doctest: rdkit.Chem.BRICS.FindBRICSBonds 208: ---------------------------------------------------------------------- 208: Traceback (most recent call last): 208: File "/usr/lib/python3.11/doctest.py", line 2222, in runTest 208: raise self.failureException(self.format_failure(new.getvalue())) 208: AssertionError: Failed doctest test for rdkit.Chem.BRICS.FindBRICSBonds 208: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/BRICS.py", line 237, in FindBRICSBonds 208: 208: ---------------------------------------------------------------------- 208: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/BRICS.py", line 256, in rdkit.Chem.BRICS.FindBRICSBonds 208: Failed example: 208: res = list(FindBRICSBonds(m,randomizeOrder=True)) 208: Exception raised: 208: Traceback (most recent call last): 208: File "/usr/lib/python3.11/doctest.py", line 1351, in __run 208: exec(compile(example.source, filename, "single", 208: File "", line 1, in 208: res = list(FindBRICSBonds(m,randomizeOrder=True)) 208: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 208: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/BRICS.py", line 291, in FindBRICSBonds 208: random.shuffle(indices, random=random.random) 208: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 208: 208: 208: ---------------------------------------------------------------------- 208: Ran 25 tests in 14.241s 208: 208: FAILED (failures=1) 208: .. 208: ---------------------------------------------------------------------- 208: Ran 2 tests in 0.056s 208: 208: OK 123: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] 208: ..s... 208: ---------------------------------------------------------------------- 208: Ran 6 tests in 0.904s 208: 208: OK (skipped=1) 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] 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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 0.138s 208: 208: OK 208: .................. 208: ---------------------------------------------------------------------- 208: Ran 18 tests in 0.842s 208: 208: OK 208: ... 208: ---------------------------------------------------------------------- 208: Ran 3 tests in 0.130s 208: 208: OK 208: ........ 208: ---------------------------------------------------------------------- 208: Ran 8 tests in 0.035s 208: 208: OK 208: .. 208: ---------------------------------------------------------------------- 208: Ran 2 tests in 0.024s 208: 208: OK 208: .. 208: ---------------------------------------------------------------------- 208: Ran 2 tests in 0.025s 208: 208: OK 208: . 208: ---------------------------------------------------------------------- 208: Ran 1 test in 0.099s 208: 208: OK 208: ........ 208: ---------------------------------------------------------------------- 208: Ran 8 tests in 0.002s 208: 208: OK 208: ... 208: ---------------------------------------------------------------------- 208: Ran 3 tests in 0.004s 208: 208: OK 208: ... 208: ---------------------------------------------------------------------- 208: Ran 3 tests in 0.002s 208: 208: OK 208: ...E 208: ====================================================================== 208: ERROR: test_CombineFeatMaps (__main__.TestCase.test_CombineFeatMaps) 208: ---------------------------------------------------------------------- 208: Traceback (most recent call last): 208: File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/FeatMaps/UnitTestFeatMapUtils.py", line 257, in test_CombineFeatMaps 208: fm12 = FeatMapUtils.CombineFeatMaps(fm1, fm2) 208: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 208: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/FeatMaps/FeatMapUtils.py", line 235, in CombineFeatMaps 208: __copyAll(res, fm1, fm2) 208: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/FeatMaps/FeatMapUtils.py", line 61, in __copyAll 208: res.AddFeatPoint(copy.deepcopy(feat)) 208: ^^^^^^^^^^^^^^^^^^^ 208: File "/usr/lib/python3.11/copy.py", line 161, in deepcopy 208: rv = reductor(4) 208: ^^^^^^^^^^^ 208: RuntimeError: Incomplete pickle support (__getstate_manages_dict__ not set) 208: 208: ---------------------------------------------------------------------- 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 0.019s 208: 208: OK 208: .... 208: ---------------------------------------------------------------------- 208: Ran 4 tests in 0.020s 208: 208: OK 208: .... 208: ---------------------------------------------------------------------- 208: Ran 4 tests in 3.636s 208: 208: OK 208: .......... 208: ---------------------------------------------------------------------- 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 208: 208: OK 208: .......... 208: ---------------------------------------------------------------------- 208: Ran 10 tests in 0.004s 208: 208: OK 208: ....E 208: ====================================================================== 208: ERROR: testOrderBug2 (__main__.TestCase.testOrderBug2) 208: ---------------------------------------------------------------------- 208: Traceback (most recent call last): 208: File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/Pharm2D/UnitTestGobbi.py", line 150, in testOrderBug2 208: m2 = Randomize.RandomizeMol(m1) 208: ^^^^^^^^^^^^^^^^^^^^^^^^^^ 208: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/Randomize.py", line 53, in RandomizeMol 208: mb = RandomizeMolBlock(mb) 208: ^^^^^^^^^^^^^^^^^^^^^ 208: File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/Randomize.py", line 29, in RandomizeMolBlock 208: random.shuffle(order, random=random.random) 208: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 208: 208: ---------------------------------------------------------------------- 208: Ran 5 tests in 0.051s 208: 208: FAILED (errors=1) 208: !!! TEST FAILURE: python UnitTestGobbi.py {} 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 8.478s 208: 208: OK 208: mol_197 208: 218.57,35.89,110.98,11.56,110.32,11.04,95.23,10.25,0.00 208: mol_223 208: 243.72,7.16,134.83,1.04,134.76,1.04,85.56,0.35,0.00 208: mol_269 208: 216.07,5.35,104.90,0.84,103.75,0.86,89.27,0.92,6.00 208: . 208: ---------------------------------------------------------------------- 208: Ran 1 test in 0.000s 208: 208: OK 208: ...[16:06:11] 208: 208: **** 208: Pre-condition Violation 208: molecule has no conformers 208: Violation occurred on line 37 in file ./Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp 208: Failed Expression: dp_mol->getNumConformers() 208: **** 208: 208: . 208: ---------------------------------------------------------------------- 208: Ran 4 tests in 0.026s 208: 208: OK 208: .. 208: ---------------------------------------------------------------------- 208: Ran 2 tests in 17.217s 208: 208: OK 208: .. 208: ---------------------------------------------------------------------- 208: Ran 2 tests in 0.118s 208: 208: OK 208: ... 208: ---------------------------------------------------------------------- 208: Ran 3 tests in 0.015s 208: 208: OK 208: .... 208: ---------------------------------------------------------------------- 208: Ran 4 tests in 0.023s 208: 208: OK 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 0.491s 208: 208: OK 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 0.486s 208: 208: OK (skipped=7) 208: sss. 208: ---------------------------------------------------------------------- 208: Ran 4 tests in 1.014s 208: 208: OK (skipped=3) 208: sss 208: ---------------------------------------------------------------------- 208: Ran 3 tests in 0.000s 208: 208: OK (skipped=3) 208: .......... 208: ---------------------------------------------------------------------- 208: Ran 10 tests in 0.931s 208: 208: OK 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 0.029s 208: 208: OK 208: .... 208: ---------------------------------------------------------------------- 208: Ran 4 tests in 0.014s 208: 208: OK 208: .................... 208: ---------------------------------------------------------------------- 208: Ran 20 tests in 0.144s 208: 208: OK 208: !!! TEST FAILURE: python UnitTestGraphDescriptors_2.py {} 208: !!! TEST FAILURE: python UnitTestMol3D.py {} 208: !!! TEST FAILURE: python UnitTestCatalog.py {} 208: !!! TEST FAILURE: python UnitTestDescriptors.py {} 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 138.81 sec ....... ---------------------------------------------------------------------- Ran 7 tests in 0.147s OK ...... ---------------------------------------------------------------------- Ran 6 tests in 0.059s OK ....[16:04:18] **** Pre-condition Violation valence not defined for atoms not associated with molecules Violation occurred on line 422 in file ./Code/GraphMol/Atom.cpp Failed Expression: dp_mol **** . ---------------------------------------------------------------------- Ran 5 tests in 0.017s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.012s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.012s OK ...................... ---------------------------------------------------------------------- Ran 22 tests in 0.039s OK .....s..........E......ss ====================================================================== ERROR: testIpc (__main__.TestCase.testIpc) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/UnitTestGraphDescriptors_2.py", line 112, in testIpc Ipc = GraphDescriptors.Ipc(m, forceDMat=1) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/GraphDescriptors.py", line 124, in Ipc cPoly = abs(Graphs.CharacteristicPolynomial(mol, adjMat)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/Graphs.py", line 43, in CharacteristicPolynomial res = numpy.zeros(nAtoms + 1, numpy.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 25 tests in 0.180s FAILED (errors=1, skipped=3) ..s ---------------------------------------------------------------------- Ran 3 tests in 0.219s OK (skipped=1) ................................... ---------------------------------------------------------------------- Ran 35 tests in 1.058s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.028s OK . ---------------------------------------------------------------------- Ran 1 test in 0.018s OK ....... ---------------------------------------------------------------------- Ran 7 tests in 0.064s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.060s OK .ss.ss....... ---------------------------------------------------------------------- Ran 13 tests in 1.856s OK (skipped=4) [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 [16:05:20] WARNING: More than one matching pattern found - picking one .[16:05:20] WARNING: More than one matching pattern found - picking one ... ====================================================================== FAIL: testEnumerateStereoisomersRandomSamplingShouldBeDeterministicAndPortable (__main__.TestCase.testEnumerateStereoisomersRandomSamplingShouldBeDeterministicAndPortable) ---------------------------------------------------------------------- Traceback (most recent call last): 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' 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 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'} .....E.. ====================================================================== ERROR: test7ScoreMolecules (__main__.TestCase.test7ScoreMolecules) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/UnitTestCatalog.py", line 176, in test7ScoreMolecules scores, obls = BuildFragmentCatalog.ScoreMolecules(suppl, cat, acts=self.list2Acts, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/BuildFragmentCatalog.py", line 164, in ScoreMolecules resTbl = numpy.zeros((nBits, 2, nActs), numpy.int) ^^^^^^^^^ File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ raise AttributeError(__former_attrs__[attr]) AttributeError: module 'numpy' has no attribute 'int'. `np.int` was a deprecated alias for the builtin `int`. To avoid this error in existing code, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information. 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 8 tests in 0.118s FAILED (errors=1) Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/UnitTestDescriptors.py", line 57, in testBadAtomHandling v = fn(m) ^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/GraphDescriptors.py", line 124, in Ipc cPoly = abs(Graphs.CharacteristicPolynomial(mol, adjMat)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/Graphs.py", line 43, in CharacteristicPolynomial res = numpy.zeros(nAtoms + 1, numpy.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 FTraceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/UnitTestDescriptors.py", line 44, in testGithub1287 _ = fn(m) ^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/GraphDescriptors.py", line 124, in Ipc cPoly = abs(Graphs.CharacteristicPolynomial(mol, adjMat)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/Graphs.py", line 43, in CharacteristicPolynomial res = numpy.zeros(nAtoms + 1, numpy.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 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) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/UnitTestDescriptors.py", line 57, in testBadAtomHandling v = fn(m) ^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/GraphDescriptors.py", line 124, in Ipc cPoly = abs(Graphs.CharacteristicPolynomial(mol, adjMat)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/Graphs.py", line 43, in CharacteristicPolynomial res = numpy.zeros(nAtoms + 1, numpy.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 During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/UnitTestDescriptors.py", line 64, in testBadAtomHandling raise AssertionError('SMILES: %s; Descriptor: %s' % (smi, nm)) AssertionError: SMILES: CC[Pu]; Descriptor: Ipc ====================================================================== FAIL: testGithub1287 (__main__.TestCase.testGithub1287) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/UnitTestDescriptors.py", line 44, in testGithub1287 _ = fn(m) ^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/GraphDescriptors.py", line 124, in Ipc cPoly = abs(Graphs.CharacteristicPolynomial(mol, adjMat)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/Graphs.py", line 43, in CharacteristicPolynomial res = numpy.zeros(nAtoms + 1, numpy.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 During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/UnitTestDescriptors.py", line 48, in testGithub1287 raise AssertionError('SMILES: %s; Descriptor: %s' % (smi, nm)) AssertionError: SMILES: CCC; Descriptor: Ipc ---------------------------------------------------------------------- Ran 14 tests in 3.598s FAILED (failures=2) .... ---------------------------------------------------------------------- Ran 4 tests in 1.500s OK ...... ---------------------------------------------------------------------- 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. antibiotics = antibiotics.append({'Smiles':'CC1(C(N2C(S1)C(C2=O)NC(=O)CC3=CC=CC=C3)C(=O)O)C', :1: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. antibiotics = antibiotics.append({ :1: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. antibiotics = antibiotics.append({ .......s..s........ ---------------------------------------------------------------------- Ran 26 tests in 2.593s OK (skipped=2) .............F[16:05:49] WARNING: More than one matching pattern found - picking one [16:05:49] WARNING: More than one matching pattern found - picking one ..[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) Doctest: rdkit.Chem.BRICS.FindBRICSBonds ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3.11/doctest.py", line 2222, in runTest raise self.failureException(self.format_failure(new.getvalue())) AssertionError: Failed doctest test for rdkit.Chem.BRICS.FindBRICSBonds File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/BRICS.py", line 237, in FindBRICSBonds ---------------------------------------------------------------------- File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/BRICS.py", line 256, in rdkit.Chem.BRICS.FindBRICSBonds Failed example: res = list(FindBRICSBonds(m,randomizeOrder=True)) Exception raised: Traceback (most recent call last): File "/usr/lib/python3.11/doctest.py", line 1351, in __run exec(compile(example.source, filename, "single", File "", line 1, in res = list(FindBRICSBonds(m,randomizeOrder=True)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/BRICS.py", line 291, in FindBRICSBonds random.shuffle(indices, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- Ran 25 tests in 14.241s FAILED (failures=1) .. ---------------------------------------------------------------------- Ran 2 tests in 0.056s OK ..s... ---------------------------------------------------------------------- Ran 6 tests in 0.904s OK (skipped=1) ..[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 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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 0.138s OK .................. ---------------------------------------------------------------------- Ran 18 tests in 0.842s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.130s OK ........ ---------------------------------------------------------------------- Ran 8 tests in 0.035s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.024s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.025s OK . ---------------------------------------------------------------------- Ran 1 test in 0.099s OK ........ ---------------------------------------------------------------------- Ran 8 tests in 0.002s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.004s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.002s OK ...E ====================================================================== ERROR: test_CombineFeatMaps (__main__.TestCase.test_CombineFeatMaps) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/FeatMaps/UnitTestFeatMapUtils.py", line 257, in test_CombineFeatMaps fm12 = FeatMapUtils.CombineFeatMaps(fm1, fm2) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/FeatMaps/FeatMapUtils.py", line 235, in CombineFeatMaps __copyAll(res, fm1, fm2) File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/FeatMaps/FeatMapUtils.py", line 61, in __copyAll res.AddFeatPoint(copy.deepcopy(feat)) ^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.11/copy.py", line 161, in deepcopy rv = reductor(4) ^^^^^^^^^^^ RuntimeError: Incomplete pickle support (__getstate_manages_dict__ not set) ---------------------------------------------------------------------- Ran 4 tests in 0.006s FAILED (errors=1) !!! TEST FAILURE: python UnitTestFeatMapUtils.py {} ....... ---------------------------------------------------------------------- Ran 7 tests in 0.019s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.020s OK .... ---------------------------------------------------------------------- Ran 4 tests in 3.636s OK .......... ---------------------------------------------------------------------- Ran 10 tests in 0.057s OK . ---------------------------------------------------------------------- Ran 1 test in 0.000s OK .......... ---------------------------------------------------------------------- Ran 10 tests in 0.004s OK ....E ====================================================================== ERROR: testOrderBug2 (__main__.TestCase.testOrderBug2) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/Pharm2D/UnitTestGobbi.py", line 150, in testOrderBug2 m2 = Randomize.RandomizeMol(m1) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/Randomize.py", line 53, in RandomizeMol mb = RandomizeMolBlock(mb) ^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu/rdkit/Chem/Randomize.py", line 29, in RandomizeMolBlock random.shuffle(order, random=random.random) TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- Ran 5 tests in 0.051s FAILED (errors=1) !!! TEST FAILURE: python UnitTestGobbi.py {} ................[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 8.478s OK mol_197 218.57,35.89,110.98,11.56,110.32,11.04,95.23,10.25,0.00 mol_223 243.72,7.16,134.83,1.04,134.76,1.04,85.56,0.35,0.00 mol_269 216.07,5.35,104.90,0.84,103.75,0.86,89.27,0.92,6.00 . ---------------------------------------------------------------------- Ran 1 test in 0.000s OK ...[16:06:11] **** Pre-condition Violation molecule has no conformers Violation occurred on line 37 in file ./Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp Failed Expression: dp_mol->getNumConformers() **** . ---------------------------------------------------------------------- Ran 4 tests in 0.026s OK .. ---------------------------------------------------------------------- Ran 2 tests in 17.217s OK .. ---------------------------------------------------------------------- Ran 2 tests in 0.118s OK ... ---------------------------------------------------------------------- Ran 3 tests in 0.015s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.023s OK .....[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 0.491s OK 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 0.486s OK (skipped=7) sss. ---------------------------------------------------------------------- Ran 4 tests in 1.014s OK (skipped=3) sss ---------------------------------------------------------------------- Ran 3 tests in 0.000s OK (skipped=3) .......... ---------------------------------------------------------------------- Ran 10 tests in 0.931s OK ..[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 0.029s OK .... ---------------------------------------------------------------------- Ran 4 tests in 0.014s OK .................... ---------------------------------------------------------------------- Ran 20 tests in 0.144s OK !!! TEST FAILURE: python UnitTestGraphDescriptors_2.py {} !!! TEST FAILURE: python UnitTestMol3D.py {} !!! TEST FAILURE: python UnitTestCatalog.py {} !!! TEST FAILURE: python UnitTestDescriptors.py {} !!! TEST FAILURE: python UnitTestDocTestsChem.py {} !!! TEST FAILURE: python test_list.py {'dir': 'FeatMaps'} !!! TEST FAILURE: python test_list.py {'dir': 'Pharm2D'} 96% tests passed, 8 tests failed out of 208 Total Test time (real) = 223.90 sec The following tests FAILED: 11 - pyBV (Failed) 22 - pyAlignment (Failed) 28 - pyDistGeom (Failed) 51 - pyDepictor (Failed) 136 - moldraw2DTest1 (Subprocess aborted) 140 - testFMCS (Subprocess aborted) 202 - pythonTestDirML (Failed) 208 - pythonTestDirChem (Failed) 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 -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 dh_testroot -O--buildsystem=cmake -O--parallel dh_prep -O--buildsystem=cmake -O--parallel dh_installdirs -O--buildsystem=cmake -O--parallel 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 -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 make[3]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' Install the project... /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/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: 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/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/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/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/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/pilfonts -- 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/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/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-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-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: 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/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: 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/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/courier-14.pbm -- 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/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: 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/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-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/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/pdfutils.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: 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/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/FunctionalGroups.txt -- 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: 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/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/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/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 -- 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/Descriptors.sqlt -- 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/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/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/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 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/cmake/rdkit/rdkit-targets.cmake -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/cmake/rdkit/rdkit-targets-none.cmake -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/cmake/rdkit/rdkit-config.cmake -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/cmake/rdkit/rdkit-config-version.cmake -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/CoordGen.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdCoordGen.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitga.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitga.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitga.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitRDGeneral.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitRDGeneral.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitRDGeneral.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/Exceptions.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/BadFileException.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/BoostStartInclude.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/BoostEndInclude.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/Dict.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/FileParseException.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/Invariant.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/RDAny.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/RDValue.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/RDValue-doublemagic.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/RDValue-taggedunion.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/RDLog.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/RDProps.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/RDThreads.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/StreamOps.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/types.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/utils.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/versions.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/RDConfig.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/LocaleSwitcher.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/Ranking.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/hanoiSort.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/RDExportMacros.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/export.h -- 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/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 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDBoost/Wrap.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDBoost/PySequenceHolder.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDBoost/list_indexing_suite.hpp -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDBoost/python.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDBoost/boost_numpy.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDBoost/python_streambuf.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/rdBase.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitRDStreams.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitRDStreams.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitRDStreams.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDStreams/streams.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitDataStructs.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitDataStructs.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitDataStructs.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/DataStructs/base64.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/DataStructs/BitOps.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/DataStructs/BitVect.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/DataStructs/BitVects.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/DataStructs/BitVectUtils.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/DataStructs/DatastructsException.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/DataStructs/DatastructsStreamOps.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/DataStructs/DiscreteDistMat.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/DataStructs/DiscreteValueVect.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/DataStructs/ExplicitBitVect.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/DataStructs/SparseBitVect.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/DataStructs/SparseIntVect.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/DataStructs/FPBReader.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/DataStructs/MultiFPBReader.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/cDataStructs.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitRDGeometryLib.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitRDGeometryLib.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitRDGeometryLib.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Geometry/Grid3D.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Geometry/GridUtils.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Geometry/point.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Geometry/Transform2D.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Geometry/Transform3D.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Geometry/Transform.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Geometry/UniformGrid3D.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Geometry/Utils.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Geometry/rdGeometry.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Numerics/Matrix.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Numerics/SquareMatrix.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Numerics/SymmMatrix.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Numerics/Vector.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Numerics/Conrec.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitAlignment.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitAlignment.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitAlignment.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Numerics/Alignment/AlignPoints.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Numerics/rdAlignment.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitEigenSolvers.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitEigenSolvers.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitEigenSolvers.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Numerics/EigenSolvers/PowerEigenSolver.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitOptimizer.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitOptimizer.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitOptimizer.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Numerics/Optimizer/BFGSOpt.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitForceField.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitForceField.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitForceField.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/Contrib.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/ForceField.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/UFF/AngleBend.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/UFF/BondStretch.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/UFF/Contribs.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/UFF/DistanceConstraint.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/UFF/AngleConstraint.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/UFF/TorsionConstraint.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/UFF/PositionConstraint.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/UFF/Nonbonded.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/UFF/Params.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/UFF/Inversion.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/UFF/TorsionAngle.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/AngleBend.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/BondStretch.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/StretchBend.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/OopBend.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/TorsionAngle.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/Nonbonded.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/Contribs.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/DistanceConstraint.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/AngleConstraint.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/TorsionConstraint.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/PositionConstraint.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ForceField/MMFF/Params.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ForceField/rdForceField.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitDistGeometry.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitDistGeometry.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitDistGeometry.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/DistGeom/BoundsMatrix.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/DistGeom/ChiralSet.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/DistGeom/ChiralViolationContrib.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/DistGeom/DistGeomUtils.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/DistGeom/DistViolationContrib.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/DistGeom/FourthDimContrib.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/DistGeom/TriangleSmooth.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DistanceGeometry/DistGeom.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitCatalogs.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitCatalogs.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitCatalogs.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Catalogs/CatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Catalogs/Catalog.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Catalogs/CatalogParams.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitGraphMol.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitGraphMol.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitGraphMol.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Atom.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/atomic_data.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/AtomIterators.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Bond.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/BondIterators.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Canon.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Chirality.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Conformer.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/details.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/GraphMol.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolOps.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolPickler.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/PeriodicTable.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/QueryAtom.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/QueryBond.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/QueryOps.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/RDKitBase.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/RDKitQueries.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Resonance.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/RingInfo.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Rings.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ROMol.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/RWMol.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/SanitException.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/SubstanceGroup.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/StereoGroup.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MonomerInfo.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/new_canon.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolBundle.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitDepictor.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitDepictor.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitDepictor.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Depictor/DepictUtils.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Depictor/EmbeddedFrag.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Depictor/RDDepictor.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdDepictor.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitSmilesParse.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitSmilesParse.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitSmilesParse.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/primes.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmartsWrite.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesParse.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesParseOps.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesWrite.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitFileParsers.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitFileParsers.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitFileParsers.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/CDXMLParser.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileParsers.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileParserUtils.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolFileStereochem.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolSupplier.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolWriters.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/SequenceParsers.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/SequenceWriters.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/GeneralFileReader.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedMolSupplier.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedSDMolSupplier.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/PNGParser.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitSubstructMatch.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitSubstructMatch.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitSubstructMatch.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Substruct/SubstructMatch.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Substruct/SubstructUtils.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitGenericGroups.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitGenericGroups.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitGenericGroups.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/GenericGroups/GenericGroups.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitChemReactions.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitChemReactions.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitChemReactions.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Reaction.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionParser.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionPickler.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionFingerprints.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionUtils.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionRunner.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/PreprocessRxn.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/SanitizeRxn.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/Enumerate.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerateBase.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/CartesianProduct.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/RandomSample.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdChemReactions.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitChemTransforms.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitChemTransforms.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitChemTransforms.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ChemTransforms/ChemTransforms.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ChemTransforms/MolFragmenter.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitTautomerQuery.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitTautomerQuery.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitTautomerQuery.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/TautomerQuery/TautomerQuery.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdTautomerQuery.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitSubgraphs.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitSubgraphs.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitSubgraphs.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Subgraphs/Subgraphs.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Subgraphs/SubgraphUtils.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitFilterCatalog.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitFilterCatalog.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitFilterCatalog.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterCatalog.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterMatcherBase.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterMatchers.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdfiltercatalog.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitFragCatalog.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitFragCatalog.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitFragCatalog.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatGenerator.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatParams.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragFPGenerator.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdfragcatalog.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitDescriptors.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitDescriptors.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitDescriptors.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Crippen.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/BCUT.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Lipinski.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolDescriptors.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolSurf.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/ConnectivityDescriptors.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MQN.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/RegisterDescriptor.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Property.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/AUTOCORR2D.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Data3Ddescriptors.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolData3Ddescriptors.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/USRDescriptor.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/AtomFeat.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolDescriptors3D.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/EEM.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/PBF.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/PMI.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/AUTOCORR3D.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/RDF.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MORSE.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/GETAWAY.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/WHIM.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/CoulombMat.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdMolDescriptors.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitFingerprints.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitFingerprints.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitFingerprints.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/AtomPairs.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/Fingerprints.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MorganFingerprints.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MACCS.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MHFP.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/FingerprintGenerator.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/AtomPairGenerator.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MorganGenerator.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/RDKitFPGenerator.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/TopologicalTorsionGenerator.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/FingerprintUtil.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdFingerprintGenerator.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdMHFPFingerprint.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitPartialCharges.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitPartialCharges.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitPartialCharges.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/PartialCharges/GasteigerCharges.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/PartialCharges/GasteigerParams.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdPartialCharges.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolTransforms.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolTransforms.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolTransforms.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolTransforms/MolTransforms.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdMolTransforms.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/FFConvenience.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/UFF/Builder.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/UFF/UFF.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/Builder.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/MMFF.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdForceFieldHelpers.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/DistGeomHelpers/Embedder.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdDistGeom.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolAlign.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolAlign.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolAlign.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitO3AAlign.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitO3AAlign.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitO3AAlign.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolAlign/AlignMolecules.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolAlign/O3AAlignMolecules.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdMolAlign.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/FeatureParser.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeature.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdMolChemicalFeatures.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitShapeHelpers.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitShapeHelpers.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitShapeHelpers.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ShapeHelpers/ShapeEncoder.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ShapeHelpers/ShapeUtils.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdShapeHelpers.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolCatalog.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolCatalog.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolCatalog.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalog.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdMolCatalog.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2D.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DSVG.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2Dwx.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DJS.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DUtils.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DHelpers.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolDraw2D.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolDraw2D.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolDraw2D.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DCairo.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/rdMolDraw2D.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitFMCS.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitFMCS.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitFMCS.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FMCS/FMCS.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/FMCS/Graph.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdFMCS.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolHash.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolHash.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolHash.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolHash/MolHash.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolHash/nmmolhash.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdMolHash.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMMPA.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMMPA.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMMPA.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MMPA/MMPA.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdMMPA.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitCIPLabeler.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitCIPLabeler.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitCIPLabeler.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/CIPLabeler/CIPLabeler.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/CIPLabeler/TooManyNodesException.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdCIPLabeler.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitDeprotect.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitDeprotect.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitDeprotect.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Deprotect/Deprotect.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdDeprotect.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitReducedGraphs.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitReducedGraphs.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitReducedGraphs.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ReducedGraphs/ReducedGraphs.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdReducedGraphs.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitTrajectory.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitTrajectory.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitTrajectory.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Trajectory/Snapshot.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Trajectory/Trajectory.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitSubstructLibrary.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitSubstructLibrary.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitSubstructLibrary.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/SubstructLibrary.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/PatternFactory.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdSubstructLibrary.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/RGroupDecomposition/RGroupDecomp.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdRGroupDecomposition.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolInterchange.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolInterchange.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolInterchange.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolInterchange/MolInterchange.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolInterchange/details.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdMolInterchange.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitSLNParse.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitSLNParse.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitSLNParse.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/SLNParse/SLNAttribs.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/SLNParse/SLNParse.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/SLNParse/SLNParseOps.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdSLNParse.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdchem.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdmolops.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdqueries.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdmolfiles.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdtrajectory.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolStandardize.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolStandardize.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolStandardize.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/MolStandardize.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Metal.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Normalize.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Validate.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Charge.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Tautomer.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Fragment.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/rdMolStandardize.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitScaffoldNetwork.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitScaffoldNetwork.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitScaffoldNetwork.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Scaffolds/rdScaffoldNetwork.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolEnumerator.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolEnumerator.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitMolEnumerator.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolEnumerator/MolEnumerator.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/MolEnumerator/LinkNode.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdMolEnumerator.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitAbbreviations.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitAbbreviations.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitAbbreviations.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/GraphMol/Abbreviations/Abbreviations.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdAbbreviations.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Query/AndQuery.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Query/EqualityQuery.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Query/GreaterEqualQuery.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Query/GreaterQuery.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Query/LessEqualQuery.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Query/LessQuery.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Query/NullQueryAlgebra.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Query/OrQuery.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Query/Query.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Query/QueryObjects.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Query/RangeQuery.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Query/SetQuery.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Query/XOrQuery.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/Features/Feature.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/DataManip/MetricMatrixCalc/MetricFuncs.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/DataManip/MetricMatrixCalc/MetricMatrixCalc.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataManip/Metric/rdMetricMatrixCalc.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitSimDivPickers.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitSimDivPickers.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitSimDivPickers.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/SimDivPickers/DistPicker.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/SimDivPickers/LeaderPicker.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/SimDivPickers/HierarchicalClusterPicker.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/SimDivPickers/MaxMinPicker.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/SimDivFilters/rdSimDivPickers.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKithc.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKithc.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKithc.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Clustering.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitInfoTheory.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitInfoTheory.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitInfoTheory.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/rdInfoTheory.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/cQuantize.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitChemicalFeatures.so.1.2022.09.3 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitChemicalFeatures.so.1 -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitChemicalFeatures.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ChemicalFeatures/ChemicalFeature.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/ChemicalFeatures/FreeChemicalFeature.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/rdChemicalFeatures.so -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/RDPaths.py make[2]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-i686-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/rdkit-202209.3' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/rdkit-202209.3' ln -sf /usr/share/fonts/truetype/freefont/FreeSans.ttf /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/FreeSans.ttf dh_install -ppython3-rdkit /usr/lib/python3 rm -f -rf /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/docs/ rm -f -rf /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/__pycache__ dh_numpy3 dh_install mkdir -p /build/reproducible-path/rdkit-202209.3/debian/rdkit-doc/usr/share/doc/rdkit/ cp /build/reproducible-path/rdkit-202209.3/Docs/Book/_build/latex/RDKit.pdf /build/reproducible-path/rdkit-202209.3/debian/rdkit-doc/usr/share/doc/rdkit/ cp -a /build/reproducible-path/rdkit-202209.3/Docs/Book/_build/html /build/reproducible-path/rdkit-202209.3/debian/rdkit-doc/usr/share/doc/rdkit/ pg_buildext install /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit build-%v postgresql-%v-rdkit ### PostgreSQL 15 install ### make[2]: Entering directory '/build/reproducible-path/rdkit-202209.3/build-15' /bin/mkdir -p '/build/reproducible-path/rdkit-202209.3/debian/postgresql-15-rdkit/usr/lib/postgresql/15/lib' /bin/mkdir -p '/build/reproducible-path/rdkit-202209.3/debian/postgresql-15-rdkit/usr/share/postgresql/15/extension' /bin/mkdir -p '/build/reproducible-path/rdkit-202209.3/debian/postgresql-15-rdkit/usr/share/postgresql/15/extension' /usr/bin/install -c -m 755 rdkit.so '/build/reproducible-path/rdkit-202209.3/debian/postgresql-15-rdkit/usr/lib/postgresql/15/lib/rdkit.so' /usr/bin/install -c -m 644 /build/reproducible-path/rdkit-202209.3/Code/PgSQL/rdkit/rdkit.control '/build/reproducible-path/rdkit-202209.3/debian/postgresql-15-rdkit/usr/share/postgresql/15/extension/' /usr/bin/install -c -m 644 rdkit--4.2.0.sql '/build/reproducible-path/rdkit-202209.3/debian/postgresql-15-rdkit/usr/share/postgresql/15/extension/' /bin/mkdir -p '/build/reproducible-path/rdkit-202209.3/debian/postgresql-15-rdkit/usr/lib/postgresql/15/lib/bitcode/rdkit' /bin/mkdir -p '/build/reproducible-path/rdkit-202209.3/debian/postgresql-15-rdkit/usr/lib/postgresql/15/lib/bitcode'/rdkit/ /usr/bin/install -c -m 644 rdkit_io.bc '/build/reproducible-path/rdkit-202209.3/debian/postgresql-15-rdkit/usr/lib/postgresql/15/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 mol_op.bc '/build/reproducible-path/rdkit-202209.3/debian/postgresql-15-rdkit/usr/lib/postgresql/15/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 bfp_op.bc '/build/reproducible-path/rdkit-202209.3/debian/postgresql-15-rdkit/usr/lib/postgresql/15/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 sfp_op.bc '/build/reproducible-path/rdkit-202209.3/debian/postgresql-15-rdkit/usr/lib/postgresql/15/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 rxn_op.bc '/build/reproducible-path/rdkit-202209.3/debian/postgresql-15-rdkit/usr/lib/postgresql/15/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 rdkit_gist.bc '/build/reproducible-path/rdkit-202209.3/debian/postgresql-15-rdkit/usr/lib/postgresql/15/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 bfp_gist.bc '/build/reproducible-path/rdkit-202209.3/debian/postgresql-15-rdkit/usr/lib/postgresql/15/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 bfp_gin.bc '/build/reproducible-path/rdkit-202209.3/debian/postgresql-15-rdkit/usr/lib/postgresql/15/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 low_gist.bc '/build/reproducible-path/rdkit-202209.3/debian/postgresql-15-rdkit/usr/lib/postgresql/15/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 guc.bc '/build/reproducible-path/rdkit-202209.3/debian/postgresql-15-rdkit/usr/lib/postgresql/15/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 cache.bc '/build/reproducible-path/rdkit-202209.3/debian/postgresql-15-rdkit/usr/lib/postgresql/15/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 adapter.bc '/build/reproducible-path/rdkit-202209.3/debian/postgresql-15-rdkit/usr/lib/postgresql/15/lib/bitcode'/rdkit/./ /usr/bin/install -c -m 644 bitstring.bc '/build/reproducible-path/rdkit-202209.3/debian/postgresql-15-rdkit/usr/lib/postgresql/15/lib/bitcode'/rdkit/./ cd '/build/reproducible-path/rdkit-202209.3/debian/postgresql-15-rdkit/usr/lib/postgresql/15/lib/bitcode' && /usr/lib/llvm-14/bin/llvm-lto -thinlto -thinlto-action=thinlink -o rdkit.index.bc rdkit/rdkit_io.bc rdkit/mol_op.bc rdkit/bfp_op.bc rdkit/sfp_op.bc rdkit/rxn_op.bc rdkit/rdkit_gist.bc rdkit/bfp_gist.bc rdkit/bfp_gin.bc rdkit/low_gist.bc rdkit/guc.bc rdkit/cache.bc rdkit/adapter.bc rdkit/bitstring.bc make[2]: Leaving directory '/build/reproducible-path/rdkit-202209.3/build-15' ### End 15 install ### ln -sf /usr/share/javascript/jquery/jquery.js /build/reproducible-path/rdkit-202209.3/debian/rdkit-doc/usr/share/doc/rdkit//html/cppapi/jquery.js ln -sf /usr/share/javascript/jquery/jquery.js /build/reproducible-path/rdkit-202209.3/debian/rdkit-doc/usr/share/doc/rdkit//html/_static/jquery.js ln -sf /usr/share/javascript/underscore/underscore.js /build/reproducible-path/rdkit-202209.3/debian/rdkit-doc/usr/share/doc/rdkit//html/_static/underscore.js make[1]: Leaving directory '/build/reproducible-path/rdkit-202209.3' dh_installdocs -O--buildsystem=cmake -O--parallel debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/reproducible-path/rdkit-202209.3' dh_installchangelogs ReleaseNotes.md make[1]: Leaving directory '/build/reproducible-path/rdkit-202209.3' debian/rules override_dh_python3 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 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 rdGeometry.so to rdGeometry.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 I: dh_python3 fs:483: renaming rdChemicalFeatures.so to rdChemicalFeatures.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdCoordGen.so to rdCoordGen.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdDepictor.so to rdDepictor.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdDeprotect.so to rdDeprotect.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdDistGeom.so to rdDistGeom.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdFMCS.so to rdFMCS.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdFingerprintGenerator.so to rdFingerprintGenerator.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdForceFieldHelpers.so to rdForceFieldHelpers.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdMHFPFingerprint.so to rdMHFPFingerprint.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdMMPA.so to rdMMPA.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdMolAlign.so to rdMolAlign.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdMolCatalog.so to rdMolCatalog.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdMolChemicalFeatures.so to rdMolChemicalFeatures.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdMolDescriptors.so to rdMolDescriptors.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdMolEnumerator.so to rdMolEnumerator.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdMolHash.so to rdMolHash.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdMolInterchange.so to rdMolInterchange.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdMolTransforms.so to rdMolTransforms.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdPartialCharges.so to rdPartialCharges.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdRGroupDecomposition.so to rdRGroupDecomposition.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdReducedGraphs.so to rdReducedGraphs.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdSLNParse.so to rdSLNParse.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdShapeHelpers.so to rdShapeHelpers.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdSubstructLibrary.so to rdSubstructLibrary.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdTautomerQuery.so to rdTautomerQuery.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdchem.so to rdchem.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdfiltercatalog.so to rdfiltercatalog.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdfragcatalog.so to rdfragcatalog.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdmolfiles.so to rdmolfiles.cpython-311-i386-linux-gnu.so I: dh_python3 fs:483: renaming rdmolops.so to rdmolops.cpython-311-i386-linux-gnu.so 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 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 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 dh_lintian -O--buildsystem=cmake -O--parallel dh_perl -O--buildsystem=cmake -O--parallel dh_link -O--buildsystem=cmake -O--parallel dh_strip_nondeterminism -O--buildsystem=cmake -O--parallel dh_compress -O--buildsystem=cmake -O--parallel dh_fixperms -O--buildsystem=cmake -O--parallel debian/rules override_dh_missing make[1]: Entering directory '/build/reproducible-path/rdkit-202209.3' dh_missing --list-missing dh_missing: warning: usr/lib/cmake/rdkit/rdkit-config-version.cmake exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/cmake/rdkit/rdkit-config.cmake exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/cmake/rdkit/rdkit-targets-none.cmake exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/lib/cmake/rdkit/rdkit-targets.cmake exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_Correlation.csv exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_CorrMat.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_Correlation.csv exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_CorrMat.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_Correlation.csv exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/README exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/ForceField/ForceFieldTerms.new.odt exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Analysis/ForceField/UFF Parameters.ods exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/BackwardsIncompatibleChanges.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/CMakeLists.txt exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/FindMyRDKit.cmake exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example1.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example10.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example11.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example12.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example13.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example14.cpp exists in debian/tmp but is not 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but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example7.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example8.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example9.cpp exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/Cartridge.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/GettingStartedInC++.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/GettingStartedInPython.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/Install.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/Makefile exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/Overview.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/RDKit_Book.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/api-docs.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/conf.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/5ht3ligs.sdf exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/AmideBond.rxn exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/MinimalFeatures.fdef exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/README.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf.gz exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/bzr.sdf exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/bzr.smi exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/cdk2.sdf exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/chiral.mol exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/input.mol exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/invalid.mol exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/data/s1p_chembldoc89753.txt 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usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molD.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molE.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molF.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molG.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_0_im0.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_0_im1.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_0_im2.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book/images/RDKitCB_13_im0.png exists in debian/tmp but is 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is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/conf.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/index.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/introduction_jp.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_1.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_10.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_11.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_12.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_13.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_14.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_15.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_16.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_17.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_18.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_19.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_2.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_20.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_21.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_22.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_23.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_24.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_25.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_26.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_27.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_28.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_29.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_3.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_30.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_31.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_32.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_33.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_34.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_35.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_36.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_37.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_38.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_39.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_4.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_40.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_41.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_42.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_43.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_44.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_45.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_46.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_47.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_48.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_49.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_5.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_50.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_51.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_52.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_53.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_54.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_55.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_56.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_57.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_58.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_59.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_6.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_60.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_61.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_62.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_7.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_8.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_9.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Book_jp/terminology_jp.rst exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/CIPLabeling.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/Chem/FragmentCatalogs.html exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.ai exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.jpg exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.ai exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.jpg exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/CodingStandards.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/EnhancedStereo.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/SGroups.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/gsocGeneralFileReader.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_and_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_and_expand.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_or_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_and2_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_and2_expand.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_cis_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_cis_expand.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_trans_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_trans_expand.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_cis_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_or2_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_trans_base.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/logo.ai exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/logo.inkscape.svg exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/logo.lrg.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/logo.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/logo_plain.inkscape.svg exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/logo_plain.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Images/wiki/morganfp_atomenv1.png exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/FingerprintGenerators.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/MolStandardize.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-DummyCores.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GA.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GenericCores.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-MutipleCores.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-RingSubstitution.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-StereoChemTest.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-Tests.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-example-lactam.ipynb exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/Notebooks/compounds.txt exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Docs/RD.css exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/README exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/FeatFinderCLI.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/PythonFormat.py exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/README.md exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/create_deb_packages.sh exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/Scripts/test.sh exists in debian/tmp but is not installed to anywhere dh_missing: warning: usr/share/RDKit/license.txt exists in debian/tmp but is not installed to anywhere The following debhelper tools have reported what they installed (with files per package) * dh_install: librdkit-dev (56), librdkit1 (110), postgresql-15-rdkit (0), python3-rdkit (1), rdkit-data (3), rdkit-doc (0) * dh_installdocs: librdkit-dev (0), librdkit1 (0), postgresql-15-rdkit (0), python3-rdkit (0), rdkit-data (0), rdkit-doc (0) If the missing files are installed by another tool, please file a bug against it. When filing the report, if the tool is not part of debhelper itself, please reference the "Logging helpers and dh_missing" section from the "PROGRAMMING" guide for debhelper (10.6.3+). (in the debhelper package: /usr/share/doc/debhelper/PROGRAMMING.gz) Be sure to test with dpkg-buildpackage -A/-B as the results may vary when only a subset is built If the omission is intentional or no other helper can take care of this consider adding the paths to debian/not-installed. make[1]: Leaving directory '/build/reproducible-path/rdkit-202209.3' dh_dwz -a -O--buildsystem=cmake -O--parallel dh_strip -a -O--buildsystem=cmake -O--parallel dh_makeshlibs -a -O--buildsystem=cmake -O--parallel 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-doc: substitution variable ${shlibs:Depends} used, but is not 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: 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: 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: 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 '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 '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-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) dpkg-source --after-build . 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/8554 and its subdirectories I: Current time: Sat Jan 20 16:10:07 +14 2024 I: pbuilder-time-stamp: 1705716607